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WO2018018077A1 - Méthodes de traitement du cancer du sein et réactifs à cet effet - Google Patents

Méthodes de traitement du cancer du sein et réactifs à cet effet Download PDF

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Publication number
WO2018018077A1
WO2018018077A1 PCT/AU2017/050766 AU2017050766W WO2018018077A1 WO 2018018077 A1 WO2018018077 A1 WO 2018018077A1 AU 2017050766 W AU2017050766 W AU 2017050766W WO 2018018077 A1 WO2018018077 A1 WO 2018018077A1
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Prior art keywords
mirna
rnai molecule
breast cancer
iii
mir
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PCT/AU2017/050766
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English (en)
Inventor
Alex SWARBRICK
Iva NIKOLIC
Kaylene SIMPSON
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Garvan Institute of Medical Research
Peter MacCallum Cancer Institute
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Garvan Institute of Medical Research
Peter MacCallum Cancer Institute
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Priority claimed from AU2016902908A external-priority patent/AU2016902908A0/en
Application filed by Garvan Institute of Medical Research, Peter MacCallum Cancer Institute filed Critical Garvan Institute of Medical Research
Publication of WO2018018077A1 publication Critical patent/WO2018018077A1/fr
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]
    • C12N2310/141—MicroRNAs, miRNAs
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/11—Applications; Uses in screening processes for the determination of target sites, i.e. of active nucleic acids

Definitions

  • the present disclosure generally relates to methods and reagents for treating breast cancer.
  • the present disclosure relates to the use of RNA interference (RNAi) molecules, such as miRNA and precursor molecules thereof, which affect viability of breast cancer cells, and their use to treat breast cancer.
  • RNAi RNA interference
  • the present disclosure relates to the use of RNAi molecules as standalone therapeutics for treating breast cancer, as well as their use as adjunctive agents in combination with existing chemotherapeutic agents for treatment of breast cancer.
  • TNBCs triple negative breast cancers
  • PR progesterone
  • ER oestrogen
  • ERBB2/Her2 receptors ERBB2/Her2 receptors
  • MicroRNAs are a class of cellular small noncoding RNAs that act to regulate protein synthesis through messenger RNA (mRNA) destabilisation and inhibition of translation (Bushati and Cohen 2007). They are typically synthesised through the formation of long hairpin molecules, which are then processed through a series of enzymatic steps into single- stranded RNAs, around 22nt long (Ha et al, 2014). To become fully functional, the mature microRNAs associate with multiple RNA- binding proteins into the RNA-Induced Silencing Complex (RISC) where they exert their effects on specific mRNAs through hybridisation to partly complementary mRNA targets.
  • RISC RNA-Induced Silencing Complex
  • microRNAs bind mRNA through a canonical mechanism, mediated via complementarity between the 6-8nt seed of the microRNA with regions typically in the 3' UTR of the mRNA.
  • seed regions are frequently not complementary, they can be found anywhere within a transcript, or be completely absent thereby dramatically expanding the number of potential targets (Hausser et al, 2014, Nat Gen).
  • computational algorithms which generally rely on the presence of a seed-match in a transcript, are still the most widely used tools for predicting genuine microRNA targets, numerous experimental techniques for identifying microRNA targets have also been developed (Cloonan et al, 2015).
  • microRNAs control a large diversity of cellular processes, from differentiation and proliferation to cell death (Bernstein et al, 2003; Yi et al, 2008; Cimmino et al, 2005), and that their deregulation can lead to many human diseases.
  • cancer has been widely studied, as microRNAs control cancer phenotype (Lu et al. 2005) and can potentially serve as biomarkers and a novel class of cancer therapeutics (Ling et al. 2013).
  • a key challenge in this space is the identification of the most functionally relevant miRNAs to target in any given malignancy.
  • the miRNA literature is dominated by a small number of well-described miRNA that undergo expression changes or copy number alteration, which are not necessarily linked to the microRNA function in the malignant process.
  • Our knowledge of the function of miRNA in cancer is fragmented across widely divergent small-scale candidate studies, and there is even less literature attempting to rationally integrate miRNA into multi-modal or combination therapy.
  • the identification of miRNAs involved in the proliferation, differentiation and survival of breast cancer cells has the potential for the development of new therapeutic, multimodal and combination therapies for treatment of breast cancer. Summary
  • the present inventors performed functional screens with miRNA libraries in a number of different breast cancer cell lines (representing different breast cancer subtypes) to determine the effect of miRNAs on cellular viability of breast cancer cells. In so doing, the inventors have identified miRNAs with a previously unrecognised role in survival, proliferation and differentiation of breast cancer cells. In particular, the inventors have identified miRNAs which, when overexpressed or administered as a stand-alone treatment, are lethal to breast cancer cells (hereinafter referred to as 'lethal' miRNAs).
  • the inventors have also identified miRNAs which result in lethal phenotype to breast cancer cells when administered in combination with chemotherapy, including low dose e.g., IC20, chemotherapy (hereinafter referred to as 'synthetic lethal' miRNAs).
  • the present disclosure provides a method for treating breast cancer in a subject suffering therefrom, said method comprising administering to the subject a RNA interference (RNAi) molecule selected from the group consisting of: (i) a microRNA (miRNA) selected from the group of miRNAs set forth in Table 1 or Table 2;
  • RNAi RNA interference
  • miRNA microRNA
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the RNAi molecule is a lethal RNAi molecule.
  • the RNAi molecule is a lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • An exemplary lethal RNAi molecule is a miRNA selected from the group consisting of miRNAs set forth in Table 1.
  • the RNAi molecule is a synthetic lethal RNAi molecule.
  • the RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule is selected from the group consisting of:
  • a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule is selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • An exemplary synthetic lethal RNAi molecule is a miRNA selected from the group consisting of miRNAs set forth in Table 2, and preferably a miRNA set forth in rows 1-55 of Table 2.
  • a further exemplary synthetic lethal RNAi molecule is a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • miR-199a-5p or miR-29b-2-5p is a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • administration of the RNAi molecule to the subject sensitizes a breast cancer cell to a chemotherapeutic agent.
  • administration of the RNAi molecule to the subject reduces a therapeutically effective dose of a chemotherapeutic agent which is effective for treating breast cancer.
  • the therapeutically effective dose of the chemotherapeutic agent for treating breast cancer is reduced relative to a dose of the chemotherapeutic agent which is therapeutically effective in a subject who has not been, or will not be, administered the RNAi molecule.
  • the reduced dose of the chemotherapeutic agent may be a IC30 concentration of the chemotherapeutic agent.
  • the reduced dose of the chemotherapeutic agent may be a IC20 concentration of the chemotherapeutic agent.
  • the reduced dose of the chemotherapeutic agent may be a IC10 concentration of the chemotherapeutic agent.
  • an RNAi molecule which sensitizes a breast cancer cell to a chemotherapeutic agent is a synthetic lethal RNAi molecule as described herein e.g., as defined in Table 2, optionally wherein the synthetic lethal RNAi molecule is a synthetic lethal RNAi molecule as defined in rows 1-55 of Table 2.
  • a synthetic lethal RNAi molecule which sensitizes a breast cancer cell to a chemotherapeutic agent is a synthetic lethal RNAi molecule corresponding to miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, or miR-27b-3p in accordance with any example hereof.
  • a synthetic lethal RNAi molecule which sensitizes a breast cancer cell to a chemotherapeutic agent is a synthetic lethal RNAi molecule corresponding to miR- 199a-5p or miR-29b-2-5p in accordance with any example hereof.
  • the nucleic acid encoding an RNAi molecule as described herein is comprised within an expression vector e.g., a plasmid or viral particle.
  • nucleic acid encoding an RNAi molecule as described herein is comprised within an exosome or microvesicle.
  • RNAi molecule or the nucleic acid encoding an RNAi molecule as described herein is comprised within an intact minicell.
  • the method described herein further comprises administering to the subject a chemotherapeutic agent.
  • the method may comprise administering to the subject a reduced therapeutically effective dose of a chemotherapeutic agent.
  • a reduced therapeutically effective dose of the chemotherapeutic agent is one which is therapeutically effective in the treatment of breast cancer and reduced relative to a dose of the chemotherapeutic agent which is therapeutically effective in a subject who has not been, or will not be, administered the RNAi molecule.
  • an RNAi molecule which may be administered in combination with a chemotherapeutic agent and which reduces a therapeutically effective dose of the chemotherapeutic agent is a synthetic lethal RNAi molecule as described herein e.g., as defined in Table 2, optionally wherein the synthetic lethal RNAi molecule is a synthetic lethal RNAi molecule as defined in rows 1-55 of Table 2.
  • a synthetic lethal RNAi molecule which reduces a dose of a chemotherapeutic agent which is therapeutically effective for treating breast cancer is a synthetic lethal RNAi molecule corresponding to miR- 199a-5p, miR-29b-2-5p, miR- 3151, miR-27a-3p, or miR-27b-3p in accordance with any example hereof.
  • a synthetic lethal RNAi molecule which reduces a dose of a chemotherapeutic agent which is therapeutically effective for treating breast cancer is a synthetic lethal RNAi molecule corresponding to miR-199a-5p or miR-29b-2-5p in accordance with any example hereof.
  • the chemotherapeutic agent and the RNAi molecule are administered together. In one example, the chemotherapeutic agent and the RNAi molecule are administered concurrently. In one example, the chemotherapeutic agent and the RNAi molecule are administered sequentially, in any order.
  • the subject has previously received treatment with a chemotherapeutic agent.
  • the breast cancer is refractory to treatment with the chemotherapeutic agent in the absence of adjunctive treatment with the RNAi molecule.
  • the breast cancer is recurrent.
  • the breast cancer to be treated may be any breast cancer subtype, for example, Triple Negative Breast Cancer (TNBC), HER2 type breast cancer, Luminal A subtype breast cancer or Luminal B subtype breast cancer.
  • TNBC Triple Negative Breast Cancer
  • HER2 type breast cancer Luminal A subtype breast cancer or Luminal B subtype breast cancer.
  • the breast cancer may be non-resectable.
  • the chemotherapeutic agent may be selected from a vinca alkaloid, a taxane, a platinum-based agent, or an anthracycline.
  • the chemotherapeutic agent is a vinca alkaloid e.g., vincristine, vinblastine, vinorelbine or vindesine.
  • the chemotherapeutic agent is a taxane e.g., paclitaxel, docetaxel and cabazitaxel.
  • the chemotherapeutic agent is a platinum- based agent e.g., cisplatin, carboplatin, oxaliplatin or nedaplatin.
  • the chemotherapeutic agent is an anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • RNAi RNA interference
  • the present disclosure also provides for use of a RNA interference (RNAi) molecule in the preparation of a medicament for treating breast cancer in a subject suffering therefrom, wherein the RNAi molecule is selected from the group consisting of:
  • RNA selected from the group of miRNAs set forth in Table 1 or Table 2;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the disclosure provides for use of a lethal RNAi molecule in the preparation of the medicament.
  • the RNAi molecule may be a lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • Exemplary lethal RNAi molecules useful in the preparation of a medicament of the disclosure include miRNAs selected from the group consisting of miRNAs set forth in Table 1.
  • the disclosure provides for use of a synthetic lethal RNAi molecule in the preparation of the medicament.
  • the RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule useful in the preparation of a medicament of the disclosure is selected from the group consisting of:
  • a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule useful in the preparation of a medicament of the disclosure is selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • An exemplary synthetic lethal RNAi molecule useful in the preparation of a medicament of the disclosure is a miRNA selected from the group consisting of miRNAs set forth in Table 2, and preferably a miRNA set forth in rows 1-55 of Table 2.
  • a further exemplary synthetic lethal RNAi molecule useful in the preparation of a medicament of the disclosure is a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • a miR-199a-5p or miR-29b-2-5p is selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the medicament may sensitize a breast cancer cell to a chemotherapeutic agent. Accordingly, treating breast cancer in the subject with the medicament may comprise sensitizing a breast cancer cell in the subject to a chemotherapeutic agent.
  • a medicament of the disclosure which sensitizes a breast cancer cell to a chemotherapeutic agent may comprise a synthetic lethal RNAi molecule as described herein e.g., as defined in Table 2, optionally wherein the synthetic lethal RNAi molecule is a synthetic lethal RNAi molecule as defined in rows
  • a medicament of the disclosure which sensitizes a breast cancer cell to a chemotherapeutic agent may comprise a synthetic lethal RNAi molecule corresponding to miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, or miR-27b-3p in accordance with any example hereof.
  • a medicament of the disclosure which sensitizes a breast cancer cell to a chemotherapeutic agent may comprise a synthetic lethal RNAi molecule corresponding to miR-199a-5p or miR-29b-
  • treating breast cancer in the subject with the medicament may comprise reducing a dose of a chemotherapeutic agent which is therapeutically effective for treating the breast cancer.
  • a medicament of the disclosure which reduces a therapeutically effective dose of a chemotherapeutic agent for treating breast cancer may comprise a synthetic lethal RNAi molecule as described herein e.g., as defined in Table 2, optionally wherein the synthetic lethal RNAi molecule is a synthetic lethal RNAi molecule as defined in rows 1-55 of Table 2.
  • a medicament of the disclosure which reduces a dose of a chemotherapeutic agent which is therapeutically effective for treating the breast cancer may comprise a synthetic lethal RNAi molecule corresponding to miR-199a-5p, miR- 29b-2-5p, miR-3151, miR-27a-3p, or miR-27b-3p in accordance with any example hereof.
  • a medicament of the disclosure which reduces a dose of a chemotherapeutic agent which is therapeutically effective for treating the breast cancer may comprise a synthetic lethal RNAi molecule corresponding to miR-199a-5p or miR- 29b-2-5p in accordance with any example hereof.
  • the nucleic acid encoding an RNAi molecule as described herein is comprised in the medicament within an expression vector e.g., a plasmid or viral particle.
  • the RNAi molecule is comprised in the medicament within an exosome or microvesicle.
  • the RNAi molecule or the nucleic acid encoding an RNAi molecule is comprised in the medicament within a minicell e.g., an intact minicell.
  • the medicament further comprises a chemotherapeutic agent.
  • the medicament of the disclosure may comprise a reduced therapeutically effective dose of a chemotherapeutic agent.
  • a reduced therapeutically effective dose of the chemotherapeutic agent is preferably one which is therapeutically effective in the treatment of breast cancer and reduced relative to a dose of the chemotherapeutic agent which is therapeutically effective in a subject who has not been, or will not be, administered the medicament comprising the RNAi molecule of the disclosure.
  • the medicament does not comprise a chemotherapeutic agent but is formulated for administration to the subject with a chemotherapeutic agent.
  • the chemotherapeutic agent and the medicament comprising the RNAi molecule may be administered together.
  • the chemotherapeutic agent and the medicament comprising the RNAi molecule may be administered concurrently.
  • the chemotherapeutic agent and the medicament comprising the RNAi molecule may be administered sequentially, in any order.
  • the subject to be treated with the medicament has previously received treatment with a chemotherapeutic agent.
  • the breast cancer is refractory to treatment with the chemotherapeutic agent in the absence of adjunctive treatment with the medicament comprising the RNAi molecule.
  • the breast cancer is recurrent.
  • the medicament may be used to treat any breast cancer subtype, for example,
  • TNBC Triple Negative Breast Cancer
  • HER2 type breast cancer Luminal A subtype breast cancer or Luminal B subtype breast cancer.
  • the breast cancer may be non-resectable.
  • the chemotherapeutic agent may be selected from a vinca alkaloid, a taxane, a platinum- based agent, or an anthracycline.
  • the chemotherapeutic agent is a vinca alkaloid e.g., vincristine, vinblastine, vinorelbine or vindesine.
  • the chemotherapeutic agent is a taxane e.g., paclitaxel, docetaxel and cabazitaxel.
  • the chemotherapeutic agent is a platinum-based agent e.g., cisplatin, carboplatin, oxaliplatin or nedaplatin.
  • the chemotherapeutic agent is an anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • Other suitable chemotherapeutic drugs for treatment of breast cancer will be known in the art.
  • RNA interference (RNAi) molecule for use in treating breast cancer in a subject suffering therefrom, wherein the RNAi molecule is selected from the group consisting of:
  • RNA selected from the group of miRNAs set forth in Table 1 or Table 2;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • the RNAi molecule for use in treating breast cancer is a lethal
  • RNAi molecule as described herein.
  • the lethal RNAi molecule for use in treating breast cancer may be selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • RNAi molecules for treating breast cancer include miRNAs selected from the group consisting of miRNAs set forth in Table 1
  • the RNAi molecule for use in treating breast cancer is a synthetic lethal RNAi molecule as described herein.
  • the RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • the synthetic lethal RNAi molecule for use in treating breast cancer may be selected from the group consisting of:
  • a miRNA selected from the group of miRNAs set forth in rows 1-55 of Table 2; (ii) a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule for use in treating breast cancer is selected from the group consisting of:
  • a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • the synthetic lethal RNAi molecule for use in treating breast cancer is selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • An exemplary synthetic lethal RNAi molecule for use in treating breast cancer is a miRNA selected from the group consisting of miRNAs set forth in Table 2, and preferably a miRNA set forth in rows 1-55 of Table 2.
  • a further exemplary synthetic lethal RNAi molecule for use in treating breast cancer is a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • a miR-199a-5p or miR-29b-2-5p is selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • treating breast cancer may comprise sensitizing a breast cancer cell to a chemotherapeutic agent.
  • the RNAi molecule described herein may be for use in sensitizing a breast cancer cell to a chemotherapeutic agent as part of treatment.
  • the RNAi molecule which sensitizes a breast cancer cell to a chemotherapeutic agent and which is for treating breast cancer may be a synthetic lethal RNAi molecule as described herein e.g., as defined in Table 2, optionally wherein the synthetic lethal RNAi molecule is a synthetic lethal RNAi molecule as defined in rows 1-55 of Table 2.
  • the RNAi molecule which sensitizes a breast cancer cell to a chemotherapeutic agent is a synthetic lethal RNAi molecule corresponding to miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, or miR-27b-3p in accordance with any example hereof.
  • the RNAi molecule which sensitizes a breast cancer cell to a chemotherapeutic agent is a synthetic lethal RNAi molecule corresponding to miR-199a-5p or miR-29b-2-5p in accordance with any example hereof.
  • treating breast cancer as described herein may comprise reducing a dose of a chemotherapeutic agent which is therapeutically effective for treating the breast cancer.
  • a chemotherapeutic agent which is therapeutically effective for treating the breast cancer.
  • an RNAi molecule for use in treating breast cancer and which reduces a dose of a chemotherapeutic agent which is therapeutically effective in treatment may be a synthetic lethal RNAi molecule as described herein e.g., as defined in Table 2, optionally wherein the synthetic lethal RNAi molecule is a synthetic lethal RNAi molecule as defined in rows 1-55 of Table 2.
  • the RNAi molecule which reduces a dose of a chemotherapeutic agent which is therapeutically effective for treating breast cancer is a synthetic lethal RNAi molecule corresponding to miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, or miR-27b-3p in accordance with any example hereof.
  • the RNAi molecule which reduces a dose of a chemotherapeutic agent which is therapeutically effective for treating breast cancer is a synthetic lethal RNAi molecule corresponding to miR-199a-5p or miR-29b-2-5p in accordance with any example hereof.
  • a nucleic acid encoding an RNAi molecule described herein which is for use in treating breast cancer is comprised within an expression vector e.g., a plasmid or viral particle.
  • the RNAi molecule described herein which is for use in treatment of breast cancer is comprised within an exosome or microvesicle.
  • the RNAi molecule or the nucleic acid encoding an RNAi molecule as described herein which is for use in treating breast cancer is comprised within a minicell e.g., an intact minicell.
  • the RNAi molecule is for treating breast cancer in combination with a chemotherapeutic agent.
  • the RNAi molecule may be formulated together with the chemotherapeutic agent.
  • the RNAi molecule is not formulated together with the chemotherapeutic agent, but is formulated such that it can be administered in combination with the chemotherapeutic agent for treatment of breast cancer.
  • the RNAi molecule may be used to treat breast cancer by administration together with the chemotherapeutic agent.
  • the RNAi molecule may be for administration concurrent with administration of the chemotherapeutic agent.
  • the RNAi molecule may be for use in treating breast cancer by administration with the chemotherapeutic agent sequentially, in any order.
  • the RNAi molecule described herein is for use in treating a subject suffering from breast cancer who has previously received treatment with a chemotherapeutic agent.
  • the RNAi molecule may be for use in treating breast cancer which is refractory to treatment with the chemotherapeutic agent e.g., in the absence of adjunctive treatment with the RNAi molecule.
  • the RNAi molecule may be for use in treating breast cancer which is recurrent.
  • RNAi molecules may be used to treat any breast cancer subtype, for example, Triple Negative Breast Cancer (TNBC), HER2 type breast cancer, Luminal A subtype breast cancer or Luminal B subtype breast cancer.
  • TNBC Triple Negative Breast Cancer
  • HER2 type breast cancer Luminal A subtype breast cancer or Luminal B subtype breast cancer.
  • the breast cancer may be non-resectable.
  • the chemotherapeutic agent may be selected from a vinca alkaloid, a taxane, a platinum- based agent, or an anthracycline.
  • the chemotherapeutic agent is a vinca alkaloid e.g., vincristine, vinblastine, vinorelbine or vindesine.
  • the chemotherapeutic agent is a taxane e.g., paclitaxel, docetaxel and cabazitaxel.
  • the chemotherapeutic agent is a platinum-based agent e.g., cisplatin, carboplatin, oxaliplatin or nedaplatin.
  • the chemotherapeutic agent is an anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • Other suitable chemotherapeutic drugs for treatment of breast cancer will be known in the art.
  • the present disclosure also provides a pharmaceutical composition
  • a pharmaceutical composition comprising one or more RNAi molecules, nucleic acids or expression vectors as described in any example hereof and a delivery vehicle suitable for delivery of the RNAi molecule to a breast cancer cell.
  • the delivery vehicle may be an intact minicell e.g., a bacterially derived intact minicell.
  • the pharmaceutical composition may comprise an intact minicell e.g., bacterially derived intact minicell, containing one or more RNAi molecules of the disclosure or one or more expression vectors encoding same.
  • the one or more RNAi molecules comprised in the pharmaceutical composition may be selected from the group consisting of:
  • RNA selected from the group of miRNAs set forth in Table 1 or Table 2;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • pharmaceutical composition comprises a lethal RNAi molecule described herein.
  • the lethal RNAi molecule may be selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • RNAi molecules which may be formulated in the
  • composition of the disclosure include miRNAs selected from the group consisting of miRNAs set forth in Table 1.
  • the pharmaceutical composition comprises a synthetic lethal RNAi molecule described herein.
  • the synthetic lethal RNAi molecule may be selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule may be selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the pharmaceutical composition comprises a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the pharmaceutical composition comprises a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • Exemplary pharmaceutical composition may comprise a miRNA selected from the group consisting of miRNAs set forth in Table 2, and preferably a miRNA set forth in rows 1-55 of Table 2.
  • a further exemplary pharmaceutical composition may comprise a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • miR-199a-5p or miR-29b-2-5p may comprise a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the pharmaceutical composition as described in any example hereof may further comprise a chemotherapeutic agent.
  • the pharmaceutical composition of the disclosure may comprise a reduced therapeutically effective dose of a chemotherapeutic agent.
  • a reduced therapeutically effective dose of the chemotherapeutic agent is one which is therapeutically effective in the treatment of breast cancer and reduced relative to a dose of the chemotherapeutic agent which is therapeutically effective in a subject who has not been, or will not be, administered the RNAi molecule of the disclosure.
  • a pharmaceutical composition which has a reduced therapeutically effective dose of a chemotherapeutic agent comprises a synthetic lethal RNAi molecule as described herein e.g., as defined in Table 2, optionally wherein the synthetic lethal RNAi molecule is a synthetic lethal RNAi molecule as defined in rows 1-55 of Table 2.
  • the pharmaceutical composition comprising a reduced dose of the chemotherapeutic agent which is therapeutically effective for treating breast cancer comprises a synthetic lethal RNAi molecule corresponding to miR-199a-5p, miR-29b- 2-5p, miR-3151, miR-27a-3p, or miR-27b-3p in accordance with any example hereof.
  • the pharmaceutical composition comprising a reduced dose of the chemotherapeutic agent which is therapeutically effective for treating breast cancer comprises a synthetic lethal RNAi molecule corresponding to miR- 199a-5p or miR- 29b-2-5p in accordance with any example hereof.
  • the pharmaceutical composition comprises a nucleic acid encoding an RNAi molecule as described herein
  • the nucleic acid is comprised within an expression vector e.g., a plasmid or viral particle.
  • the chemotherapeutic agent may be selected from a vinca alkaloid, a taxane, a platinum-based agent, or an anthracycline.
  • the chemotherapeutic agent is a vinca alkaloid e.g., vincristine, vinblastine, vinorelbine or vindesine.
  • the chemotherapeutic agent is a taxane e.g., paclitaxel, docetaxel and cabazitaxel.
  • the chemotherapeutic agent is a platinum-based agent e.g., cisplatin, carboplatin, oxaliplatin or nedaplatin.
  • the chemotherapeutic agent is an anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • Other suitable chemotherapeutic drugs for treatment of breast cancer will be known in the art.
  • the present disclosure also provides a method of preparing a pharmaceutical composition as described herein.
  • the present disclosure provides a method of preparing a pharmaceutical composition of the disclosure comprising co- incubating a plurality of intact minicells with one or more RNAi molecules, nucleic acids or expression vectors described herein in a buffer for a period sufficient to package the RNAi molecule, nucleic acid or expression vector into the minicell(s).
  • the one or more RNAi molecules may be selected from the group consisting of: (i) a microRNA (miRNA) selected from the group of miRNAs set forth in Table 1 or Table 2;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • pharmaceutical composition is prepared with a lethal RNAi molecule described herein.
  • the lethal RNAi molecule may be selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • Exemplary lethal RNAi molecules which may be used to formulate a
  • composition of the disclosure include miRNAs selected from the group consisting of miRNAs set forth in Table 1.
  • the pharmaceutical composition is prepared with a synthetic lethal RNAi molecule described herein.
  • the synthetic lethal RNAi molecule may be selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • the synthetic lethal RNAi molecule may be selected from the group consisting of:
  • a miRNA selected from the group of miRNAs set forth in rows 1-55 of Table 2; (ii) a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the pharmaceutical composition is formulated with a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • the pharmaceutical composition is formulated with a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • Exemplary synthetic lethal RNAi molecules for formulating pharmaceutical compositions of the disclosure include miRNAs selected from the group consisting of miRNAs set forth in Table 2, and preferably a miRNA set forth in rows 1-55 of Table 2.
  • a further exemplary synthetic lethal RNAi molecules for formulating pharmaceutical compositions of the disclosure include miRNAs selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p. For example, miR-199a-5p or miR-29b-2-5p.
  • the pharmaceutical composition may be formulated with any one or more of the lethal and/or synthetic lethal RNAi molecules described herein.
  • nucleic acid encoding the RNAi molecules described herein may be provided in the form of an expression vector e.g., a plasmid or viral particle.
  • the co-incubation step involves gentle shaking. In another example, the co-incubation step is static.
  • the co-incubation period is at least about half an hour, for example at least about one hour. However, any incubation time sufficient to achieve packing is contemplated.
  • the buffer comprises buffered saline, for example a 1 x phosphate buffer solution.
  • the buffered saline can be in gelatin form.
  • the co-incubation is conducted at a temperature of about 4°C to about 37°C; about 20°C to about 30°C; about 25°C; or about 37°C.
  • the co-incubation can comprise about 10 7 , 10 s , 10 9 , 10 10 , 10 11 ,
  • the present disclosure also provides a kit comprising:
  • RNA interference RNA interference
  • RNA selected from the group of miRNAs set forth in
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of
  • RNAi molecule in the first container is a lethal RNAi molecule.
  • the RNAi molecule may be a lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • Exemplary lethal RNAi molecules which may be contained in the first container include miRNAs selected from the group consisting of miRNAs set forth in Table 1.
  • the first container of the kit comprises a synthetic lethal RNAi molecule of the disclosure.
  • the RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule of the first container of the kit of the disclosure may be selected from the group consisting of:
  • a miRNA selected from the group of miRNAs set forth in rows 1-55 of Table 2; (ii) a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule of the first container of the kit of the disclosure is selected from the group consisting of:
  • a miRNA selected from the group of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • RNAi molecule of any one of (i)-(v).
  • the synthetic lethal RNAi molecule of the first container of the kit of the disclosure is selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • Exemplary synthetic lethal RNAi molecules for inclusion in the kit of the disclosure include miRNAs selected from the group consisting of miRNAs set forth in Table 2, and preferably a miRNA set forth in rows 1-55 of Table 2.
  • a further exemplary synthetic lethal RNAi molecules for inclusion in the kit of the disclosure include miRNAs selected from the group of miR-199a-5p, miR-29b-2- 5p, miR-3151, miR-27a-3p, and miR-27b-3p. For example, miR-199a-5p or miR-29b- 2-5p.
  • the nucleic acid encoding an RNAi molecule of the disclosure may be comprised within an expression vector e.g., a plasmid or viral particle.
  • the RNAi molecule is comprised within an exosome or microvesicle.
  • the RNAi molecule or the nucleic acid encoding an RNAi molecule is comprised within a minicell e.g., an intact minicell.
  • the kit described herein is for treating breast cancer. Accordingly, the present disclosure contemplates use of the subject kit for treating breast cancer e.g., by administering to a subject the RNAi molecule of the first container and the chemotherapeutic agent of the second container.
  • the chemotherapeutic agent and the RNAi molecule may be administered together.
  • the chemotherapeutic agent and the RNAi molecule may be administered concurrently.
  • the chemotherapeutic agent and the RNAi molecule may be administered sequentially.
  • the kit is for treating a subject suffering from breast cancer who has previously received treatment with a chemotherapeutic agent.
  • the kit may be for treating breast cancer which is refractory to treatment with the chemotherapeutic agent by itself e.g., in the absence of adjunctive treatment with the RNAi molecule.
  • the breast cancer may be a recurrent breast cancer.
  • the kit is for treating breast cancer which is non-resectable.
  • the breast cancer for which the kit is useful in treatment may be any breast cancer subtype, for example, Triple Negative Breast Cancer (TNBC), HER2 type breast cancer, Luminal A subtype breast cancer or Luminal B subtype breast cancer.
  • TNBC Triple Negative Breast Cancer
  • HER2 type breast cancer Luminal A subtype breast cancer or Luminal B subtype breast cancer.
  • the second container of the kit comprises a reduced therapeutically effective dose of the chemotherapeutic agent.
  • the reduced therapeutically effective dose of the chemotherapeutic agent is one which is therapeutically effective in the treatment of breast cancer and reduced relative to a dose of the chemotherapeutic agent which is therapeutically effective in a subject who has not been, or will not be, administered the RNAi molecule of the disclosure.
  • the chemotherapeutic agent may be selected from a vinca alkaloid, a taxane, a platinum- based agent, or an anthracycline.
  • the chemotherapeutic agent is a vinca alkaloid e.g., vincristine, vinblastine, vinorelbine or vindesine.
  • the chemotherapeutic agent is a taxane e.g., paclitaxel, docetaxel and cabazitaxel.
  • the chemotherapeutic agent is a platinum-based agent e.g., cisplatin, carboplatin, oxaliplatin or nedaplatin.
  • the chemotherapeutic agent is an anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • Other suitable chemotherapeutic drugs for treatment of breast cancer will be known in the art.
  • the RNAi molecule of the first container is provided in the form of a pharmaceutical composition as described in any example hereof.
  • FIG. 1 Primary screen overview in MDA-MB-231 cells. The cells were transfected with the library of microRNA mimics or inhibitors and treated with low doses (IC20) of epirubicin, docetaxel, or vehicle.
  • IC20 low doses
  • the essential microRNAs (orange) were defined as miRs killing over 50% of cells on their own while synthetic lethal miRs (black) showed potency only in conjunction with the drugs.
  • Figure 2 The synergistic effect of selected SL-miRs with epirubicin in a panel of breast cancer cell lines. The figure summarises the synthetic lethal screens with epirubicin for selected SL-miRs. All breast cancer cell lines were transfected with microRNA mimics or inhibitors under previously established conditions and treated with low doses of epirubicin (IC20-30). Each viability value was normalised to a negative OTP control on the same plate.
  • Figure 3. miR candidate expression in the SETUP trial. Triple-negative breast cancer patients underwent neoadjuvant chemotherapy including one cycle of anthracyclines and one round of docetaxel. Our main miR candidates show increased expression after chemotherapy treatment only in patients that achieved pathological complete response (pCR).
  • MDA-MB-231 cells were transfected with miR-29b-2-5p mimic in a 6-well format and treated with low doses of epirubicin (IC30) or vehicle.
  • IC30 epirubicin
  • A The phase-contrast images were taken on the incucyte microscope after 96h of drug incubation.
  • B After 48h of drug addition, the cells were stained with M30 antibody, and analysed using Canto I and Flow Jo.
  • FIG. 5 The effects of miR-29b-2-5p on epirubicin-induced cell cycle block and DNA damage.
  • the MDA-MB-231 cells were transfected with miR-29b-2-5p mimic with and without a low dose of epirubicin (IC30).
  • IC30 epirubicin
  • A, B 12h after the drug addition (if any), the cells were fixed, stained with PI, and analysed using Canto I and FlowJo.
  • C 24h following drug addition, the cells were fixed and stained using phospho gamma-H2AX antibody, and visualised on the IF microscope.
  • FIG. 6 The effects of miR-199a-5p on epirubicin-induced cell cycle block and DNA damage.
  • the MDA-MDA-MB-231 cells were transfected with miR-199a-5p mimic and treated with and without a low dos of epirubicin (IC30).
  • A, B 12h after the drug addition, the cells were fixed, stained with PI, and analysed using Canto I and FlowJo.
  • C 6h and 24h following drug addition, the cells were fixed and stained using phospho gamma-H2AX antibody, and visualised on the IF microscope.
  • the recombinant DNA, recombinant protein, cell culture, and immunological techniques utilized in the present disclosure are standard procedures, well known to those skilled in the art. Such techniques are described and explained throughout the literature in sources such as, J. Perbal, A Practical Guide to Molecular Cloning, John Wiley and Sons (1984), J. Sambrook et al. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press (1989), T.A. Brown (editor), Essential Molecular Biology: A Practical Approach, Volumes 1 and 2, IRL Press (1991), D.M. Glover and B.D. Hames (editors), DNA Cloning: A Practical Approach, Volumes 1-4, IRL Press (1995 and 1996), and F.M.
  • RNA is meant a molecule comprising at least one ribonucleotide residue.
  • ribonucleotide is meant a nucleotide with a hydroxyl group at the 2' position of a ⁇ -D-ribo-furanose moiety.
  • the terms include double-stranded RNA, single-stranded RNA, isolated RNA such as partially purified RNA, essentially pure RNA, synthetic RNA, recombinantly-produced RNA, as well as altered RNA that differs from naturally occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides.
  • Such alterations can include addition of non-nucleotide material, such as to the end(s) of the siNA or internally, for example at one or more nucleotides of the RNA.
  • Nucleotides in the RNA molecules of the instant disclosure can also comprise non-standard nucleotides, such as non-naturally occurring nucleotides or chemically synthesized nucleotides or deoxynucleotides. These altered RNAs can be referred to as analogs or analogs of naturally-occurring RNA.
  • RNA interference refers generally to RNA-dependent silencing of gene expression initiated by double stranded RNA (dsRNA) molecules in a cell's cytoplasm.
  • dsRNA double stranded RNA
  • the dsRNA molecule reduces or inhibits transcription products of a target nucleic acid sequence, thereby silencing the gene or reducing expression of that gene.
  • RNA interference molecule or "RNAi molecule” refers to a molecule that is capable of eliciting "RNA interference” or "RNAi”.
  • this term refers to a miRNA or a precursor thereof e.g., a pri-miRNA or pre- miRNA or a miRNA mimic, and in other examples this term is used to refer to a nucleic acid which encodes a miRNA or a precursor thereof of the disclosure.
  • microRNA refers to a class of small non-coding RNA molecules of between about 18 and about 25 nucleobases in length which comprise a sequence capable of hybridising to sequences within target messenger RNA transcripts (mRNAs), and which function in RNA silencing and post-transcriptional regulation of gene expression.
  • mRNAs target messenger RNA transcripts
  • a mature miRNA molecule comprises an "effector sequence” which binds to the a target mRNA sequence.
  • a miRNA also comprises a sequence which is complementary to and duplexed with the effector sequence through hydrogen bonding which is referred to herein as the "effector complement sequence”.
  • the effector sequence of the miRNA is the sequence loaded into the RISC complex and which binds to the target mRNA.
  • Target sequences for miRNA are typically found within mRNA 3'- and 5' untranslated regions (UTRs) as well as within mRNA coding regions. Some miRNAs target single mRNAs at multiple sites. miRNA seed regions are predicted to target on the order of 200 genes each, and most mRNA are targeted by multiple miRNA.
  • miRNAs which are particularly useful for treating breast cancer are described herein e.g., in Tables 1 and 2.
  • miRNAs of the disclosure can be obtained from a precursor molecule (referred to herein as a "precursor miRNA”, “pre-miRNA”, “pre- miR” or “miRNA precursor”) through natural processing routes (e.g. , using intact cells or cell lysates) or by synthetic processing routes (e.g., using isolated processing enzymes, such as isolated Dicer, Argonaut, or RNAase III). It will be appreciated that the miRNA molecule can also be produced directly by biological or chemical syntheses, without having been processed from a pre-miRNA.
  • microRNA encompasses both miRNAs produced through pre- miRNA processing by Dicer and miRNAs produced through direct biological or chemical synthesis.
  • a number of studies have looked at the base-pairing requirement between miRNA and its mRNA target for achieving efficient inhibition of translation (reviewed by Bartel (2004) Cell 116:281).
  • the first 8 nucleotides of the miRNA may be important.
  • other parts of the microRNA may also participate in mRNA binding.
  • sufficient base pairing at the 3' can compensate for insufficient pairing at the 5' (Brennecke et al., (2005) PLoS 3-e85).
  • RNA precursor means a non-coding RNA having a hairpin structure, which contains a miRNA of the disclosure.
  • a miRNA may be present in one arm of the hairpin precursor which lacks large internal loops or bulges.
  • a pre-miRNA is the product of cleavage of a primary mi-RNA transcript, (also referred to herein as a "primary miRNA”, “pri-miRNA” or “pri-miR”) by the double-stranded RNA-specific ribonuclease known as Drosha.
  • pre- miRNAs can also be produced directly by biological or chemical synthesis without having been processed from a pri-miR.
  • the pre-miRNA sequence may comprise from 45-90, 60- 80 or 60-70 nucleotides.
  • a pre-miRNA will comprise a stem or double- stranded region comprising the miRNA duplex (i.e., a region of the nucleic acid molecule that is in a double stranded conformation via hydrogen bonding between the nucleotides), and a loop region of unpaired nucleotides at the terminal end of the stem.
  • the unpaired nucleotides of the loop region of a pre-miRNA are also referred to herein as a "stem loop".
  • the duplexed region of the pre-miRNA will include the effector sequence of the miRNA (that binds to a target mRNA) hydrogen bonded to its cognate effector complement sequence
  • a pre-miRNA molecule described herein may comprise more than one miRNA of the disclosure, including a miRNA as described herein and one or more variants thereof.
  • the sequence of the pre-miRNA may also be that of the corresponding pri-miRNA molecule excluding from 0-160 nucleotides from the 5' and 3' ends of the pri- miRNA.
  • the term "pri-miRNA” means a primary miRNA transcript that is cleaved by Drosha or an equivalent protein.
  • the pri-miRNA sequence may comprise from 45-250, 55-200, 70-150 or 80-100 nucleotides.
  • the pri-miRNA may be a hairpin structure formed between a first and a second nucleic acid sequence which are substantially complementary to one another.
  • One of the first and second nucleic acid sequences will comprise the effector sequence of the mature miRNA and the other will comprise the cognate effector complement sequence.
  • the first and second nucleic acid sequence may be from 37-50 nucleotides.
  • the first and second nucleic acid sequence may be separated by a third sequence of from 4-20, 8-12 or 10 nucleotides which forms a term loop (also referred to as a stem loop).
  • the hairpin structure may have a free energy less than -25 cal/mole as calculated by the Vienna algorithm with default parameters, as described in Hofacker et al, (1994) Monatsnefte f. Chemie, 125: 167-188, the contents of which are incorporated herein.
  • miRNA mimic refers to synthetic small non-coding RNAs capable of entering the RNAi pathway and regulating gene expression.
  • synthetic miRNA refers to any type of miRNA sequence, other than an endogenous miRNA. miRNA mimics imitate the function of endogenous miRNAs and can be designed as mature, double stranded (duplex) molecules or mimic precursors e.g., pri-miRNAs or pre-miRNAs.
  • the miRNA mimic may comprise an effector sequence which is substantially identical to the effector sequence of the corresponding endogenous miRNA. miRNA mimics can be comprised of modified and/or unmodified RNA, DNA, RNA-DNA hybrids or alternative nucleic acid chemistries.
  • effector sequence is a sequence of about 18 to 25 nucleobases within the miRNA, pre-miRNA or pri- miRNA of the disclosure which is substantially complementary to a target mRNA sequence, which in the present case is associated with breast cancer (e.g., breast cancer proliferation, differentiation and survival).
  • effector complement sequence refers to the sequence within a miRNA duplex, pre-miRNA or pri-miRNA of the disclosure which is of similar length and of sufficient complementarity to the effector sequence such that it can anneal to the effector sequence to form a duplex.
  • the effector complement sequence will be substantially homologous to a region of the target mRNA transcript.
  • effector complement sequence can also be referred to as the "complement of the effector sequence" or "passenger strand”.
  • duplex refers to a region within two complementary or substantially complementary RNA sequences, or in two complementary or substantially complementary regions of a single- stranded RNA, that form base pairs with one another, either by Watson-Crick base pairing or any other manner that allows for a stabilized duplex between the nucleotide sequences that are complementary or substantially complementary. It will be understood by the skilled person that within a duplex region, 100% complementarity is not required; substantial complementarity is allowable. Substantial complementarity may include 75% or greater complementarity.
  • a single mismatch in a duplex region consisting of 19 base pairs results in 94.7% complementarity, rendering the duplex region substantially complementary.
  • two mismatches in a duplex region consisting of 19 base pairs results in 89.5% complementarity, rendering the duplex region substantially complementary.
  • three mismatches in a duplex region consisting of 19 base pairs results in 84.2% complementarity, rendering the duplex region substantially
  • nucleotides 2-8 are not located within the region corresponding to the seed region of the miRNA i.e., nucleotides 2-8.
  • a pri-miRNA or a pre-miRNA as described herein may be provided as a hairpin or stem loop structure, with a duplex region comprised of at least the effector sequence and effector complement sequence of a corresponding miRNA linked by at least between at least 2 nucleotide e.g., between 8 and 14 nucleotides, which is termed a "stem loop".
  • the term "complementary" or “complementarity” with regard to a sequence refers to a complement of the sequence by Watson-Crick base pairing, whereby guanine (G) pairs with cytosine (C), and adenine (A) pairs with either uracil (U) or thymine (T).
  • a sequence may be complementary to the entire length of another sequence, or it may be complementary to a specified portion or length of another sequence.
  • U may be present in RNA
  • T may be present in DNA. Therefore, an A within either of a RNA or DNA sequence may pair with a U in a RNA sequence or T in a DNA sequence.
  • the term “substantially complementary”, “substantial complementarity” or similar is used to indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between nucleic acid sequences e.g., between the effector sequence and the effector complement sequence or between the effector sequence and the target sequence. It is understood that the sequence of a nucleic acid need not be 100% complementary to that of its target or complement.
  • the term encompasses a sequence complementary to another sequence with the exception of an overhang. In some cases, the sequence is complementary to the other sequence with the exception of 1-2 mismatches. In some cases, the sequences are complementary except for 1 mismatch. In some cases, the sequences are
  • sequences are identical except for 2 mismatches. In other cases, the sequences are
  • sequences are identical except for 3 mismatches.
  • sequences are a sequence complementary except for 3 mismatches.
  • sequences are identical except for 4 mismatches.
  • sequences are a sequence complementary except for 4 mismatches.
  • the sequences are complementary except for 6 mismatches, and so on. However, as discussed herein, where mismatches are present, it is preferred that they are not located within the region corresponding to the seed region of the miRNA i.e., nucleotides 2-8.
  • RNAi molecule refers to an RNAi molecule which is lethal to a breast cancer cell when administered alone as a therapeutic agent.
  • RNAi molecule refers to an RNAi molecule which confers a lethal phenotype to a breast cancer cell when administered in combination with low dose (e.g., IC20) chemotherapy.
  • the dose of the chemotherapeutic agent may otherwise be insufficient to confer the lethal phenotype to the breast cancer cell in the absence of the "synthetic lethal" RNAi molecule of the disclosure.
  • the breast cancer cell may be refractory or non- responsive to treatment with the chemotherapeutic agent in the absence of the "synthetic lethal" RNAi molecule of the disclosure.
  • a nucleic acid encoding an RNAi molecule refers to a nucleic acid comprising a DNA sequence which serves as a template for transcription of the respective RNAi molecule(s) of the disclosure.
  • a “vector” will be understood to mean a vehicle for introducing a nucleic acid into a cell.
  • Vectors include, but are not limited to, plasmids, phagemids, viruses, bacteria, and vehicles derived from viral or bacterial sources.
  • a "plasmid” is a circular, double-stranded DNA molecule.
  • a useful type of vector for use in accordance with the present disclosure is a viral vector, wherein heterologous DNA sequences are inserted into a viral genome that can be modified to delete one or more viral genes or parts thereof.
  • Certain vectors are capable of autonomous replication in a host cell (e.g., vectors having an origin of replication that functions in the host cell). Other vectors can be stably integrated into the genome of a host cell, and are thereby replicated along with the host genome.
  • the term "expression vector” will be understood to mean a vector capable of expressing an RNAi molecule of the disclosure.
  • a vector for expressing an RNAi molecule of the disclosure will comprise a suitable expression construct (referred herein as a "RNAi expression construct") comprising a DNA template from which the RNAi molecule can be transcribed.
  • RNAi expression construct will be a nucleic acid comprising a DNA sequence which, when transcribed, produces an RNAi molecule of the disclosure.
  • an RNAi expression construct described herein may comprise a nucleic acid which is transcribed as a single RNA that is capable of self-annealing into a hairpin structure with a duplex region linked by at least 2 nucleotides e.g., a pre-miRNA or a pri- miRNA, to produce a single miRNA.
  • an RNAi expression construct described herein may comprise a nucleic acid which is transcribed as a single RNA that is capable of self-annealing into a hairpin structure with a duplex region linked by at least 2 nucleotides e.g., a pre-miRNA or a pri-miRNA, to produce multiple miRNAs.
  • an RNAi expression construct described herein may comprise a nucleic acid which is transcribed as multiple RNA transcripts each capable of self-annealing into a hairpin structure with a duplex region linked by at least 2 nucleotides e.g., a pre-miRNA or a pri-miRNA, and which can each be processed into one or more miRNAs of the disclosure.
  • the RNAi expression construct described herein may be operable-linked to a promoter within the expression vector.
  • operably-linked or “operable linkage” (or similar) means that the nucleic acid sequence coding for the RNAi molecule is linked to, or in association with, a regulatory sequence, e.g., a promoter, in a manner which facilitates expression of the RNAi molecule.
  • a regulatory sequence e.g., a promoter
  • Regulatory sequences include promoters, enhancers, and other expression control elements that are art-recognized and are selected to direct expression of the coding sequence.
  • minicell refers to anucleate forms of bacterial cells, engendered by a disturbance in the coordination, during binary fission, of cell division with DNA segregation. Minicells are distinct from other small vesicles that are generated and released spontaneously in certain situations and, in contrast to minicells, are not due to specific genetic rearrangements or episomal gene expression. In the context of the present disclosure, the minicells are intact since other "denuded" forms, such as spheroplasts, poroplasts, protoplasts, would leak the packaged functional nucleic acid and would not be therapeutically effective. The intact minicell membrane allows the payload to be retained within the minicell and is released intracellular within the target host mammalian cell. Accordingly, it is preferred that the minicells used in the present disclosure have intact cell walls ("intact minicells").
  • breast cancer shall be understood to include a disease that is characterized by uncontrolled growth of cells from breast tissue of a subject.
  • the breast cancer for which the composition and/or method of the disclosure may be useful may be any subtype of breast cancer, including ER negative (ER-ve) breast cancer, ER positive (ER+ve) breast cancer and TNBC.
  • estrogen receptor negative (ER-ve) breast cancer shall be understood to refer to a breast cancer which is characterised by reduced expression of the ER gene when compared to a non-cancerous sample, or an ER+ve cancerous sample, or which is characterised by a level of expression of the ER gene which is not significantly different from the level of expression of a housekeeping gene, or which is characterised by the absence of a detectable level of expression of the ER gene, or which is characterised by the absence of expression of the ER gene.
  • TNBC triple negative breast cancer
  • ER estrogen receptor
  • each one of ER, PR and HER-2 may be reduced when compared to a non-cancerous sample, or an ER+ve, PR+ve and HER2 +ve cancerous sample, or which is characterised by a level of expression of each one of ER, PR and HER-2 which is not significantly different from the level of expression of a housekeeping gene, or which is characterised by the absence of a detectable level of expression of each one of ER, PR and HER-2, or which is characterised by the absence of expression of each one of ER, PR and HER-2.
  • the term "refractory” or “refractory to treatment” in the context of breast cancer is intended to mean breast cancer which is partially or wholly non- responsive or resistant to treatment with a therapeutic agent for treating breast cancer e.g., such as a chemotherapeutic agent.
  • a therapeutic agent for treating breast cancer e.g., such as a chemotherapeutic agent.
  • a breast cancer which is refractory to a treatment may become refractory after a period of successful treatment, or may be non- responsive to treatment from the outset of treatment.
  • a “recurrent breast cancer” or “relapsed breast cancer” as referred to herein is a breast cancer which has returned in a patient who has already undergone effective initial treatment for the disease and achieved remission.
  • RNAi molecule of the disclosure alters breast cancer cells in a way that allows for more effective treatment of the breast cancer with the corresponding chemotherapeutic agent. For example, providing a cell or subject with an effective amount of an RNAi molecule of the disclosure may sensitize a breast cancer cell, which would otherwise be resistant or less-responsive, to treatment with a chemotherapeutic agent.
  • treating refers to clinical intervention designed to alter the natural course of the individual or cell being treated during the course of clinical pathology. Desirable effects of treatment include decreasing the rate of disease progression, ameliorating or palliating the disease state, and remission or improved prognosis.
  • treatment of breast cancer includes inhibiting or reducing expression of one or more genes associated with breast cancer, sensitizing a breast cancer cell to a chemotherapeutic agent, reducing a therapeutically-effective dose of a chemotherapeutic agent for treating breast cancer, improving efficacy of a chemotherapeutic agent to treat breast cancer, increasing survival time of a subject suffering from breast cancer, reducing size of a breast cancer tumour, reducing expression of one or more cancer biomarkers associated with breast cancer, reducing or slowing rate of growth of a breast cancer tumour, preventing, inhibiting or slowing spread of cancer from the primary site to other organs or tissue (metastasis), and/or reducing severity of symptoms associated with breast cancer.
  • An individual is successfully "treated", for example, if one or more of the above treatment outcomes are achieved.
  • a “therapeutically effective amount” is at least the minimum concentration or amount required to effect a measurable improvement of a particular disease (e.g., breast cancer).
  • a therapeutically effective amount herein may vary according to factors such as the disease state, age, sex, and weight of the patient, and the ability of the RNAi molecule to elicit a desired response in the individual.
  • a therapeutically effective amount is also one in which any toxic or detrimental effects of the RNAi molecule are outweighed by the therapeutically beneficial effects.
  • the "subject” or “patient” can be a human or non-human animal suffering from breast cancer.
  • the "non-human animal” may be a primate, livestock (e.g. sheep, horses, cattle, pigs, donkeys), companion animal (e.g. pets such as dogs and cats), laboratory test animal (e.g. mice, rabbits, rats, guinea pigs), performance animal (e.g. racehorses, camels, greyhounds) or captive wild animal.
  • livestock e.g. sheep, horses, cattle, pigs, donkeys
  • companion animal e.g. pets such as dogs and cats
  • laboratory test animal e.g. mice, rabbits, rats, guinea pigs
  • performance animal e.g. racehorses, camels, greyhounds
  • the subject or patient is a mammal.
  • the subject or patient is a primate.
  • the subject or patient is human.
  • the methods may further comprise a step of selecting a patient suitable for treatment with the treatment method disclosed herein.
  • the step of selecting may comprise identifying the patient as one who is suffering from, or who has suffered from breast cancer (including any of the subtypes of breast cancer described herein).
  • reduced expression refers to the absence or an observable decrease in the level of protein and/or mRNA product from the target gene.
  • the decrease does not have to be absolute, but may be a partial decrease sufficient for there to a detectable or observable change as a result of the RNAi affected by the miRNA of the disclosure.
  • the decrease can be measured by determining a decrease in the level of mRNA and/or protein product from a target nucleic acid relative to a cell lacking the RNAi molecule, and may be as little as 1 %, 5% or 10%, or may be absolute i.e., 100% inhibition.
  • the effects of the decrease may be determined by examination of the outward properties i.e., quantitative and/or qualitative phenotype of the cell or organism, and may also include detection and/or quantitation of one or more markers of breast cancer following administration of an RNAi molecule of the disclosure.
  • the present disclosure contemplates the use of certain RNAi molecules in the treatment of breast cancer.
  • the present inventors performed functional screens with miRNA libraries in breast cancer cell lines (comprising different breast cancer subtypes) to determine the effect of miRNAs on cellular viability of breast cancer cells.
  • the inventors have identified miRNAs with a previously unrecognised role in survival of breast cancer cells.
  • the inventors have identified miRNAs which, when overexpressed or administered as a stand-alone treatment, are lethal to breast cancer cells ('lethal' miRNAs).
  • the inventors have also identified that certain miRNAs screened resulted in lethal phenotype to breast cancer cells when administered in combination with low dose IC20 chemotherapy ('synthetic lethal' miRNAs).
  • RNAi molecules useful in treatment of breast cancer preferably include the seed sequence of a miRNA selected from the group of miRNAs set forth in Table 1 or Table 2.
  • RNAi molecules which are useful in the treatment of breast cancer may be selected from the group consisting of:
  • RNA selected from the group of miRNAs set forth in Table 1 or Table 2;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • a precursor miRNA pre-miRNA corresponding to a miRNA any one of (i) to (iii);
  • the RNAi molecule is a lethal RNAi molecule.
  • the RNAi molecule is a lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • the lethal RNAi molecule contemplated for use in the treatment of breast cancer may be a miRNA set forth in Table 1.
  • the RNAi molecule contemplated for use in the treatment of breast cancer is a synthetic lethal RNAi molecule.
  • Synthetic lethal RNAi molecules of the disclosure are contemplated for use in the treatment of breast cancer in combination with a chemotherapeutic agent.
  • the RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of:
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA at (i);
  • a primary miRNA corresponding to a miRNA of any one of (i) to (iii);
  • RNAi molecule of any one of (i)-(v).
  • An exemplary synthetic lethal RNAi molecule contemplated for use in the treatment of breast cancer in combination with a chemotherapeutic agent is a miRNA selected from the group of miRNAs set forth in rows 1-55 of Table 2.
  • the synthetic lethal RNAi molecule is a miRNA selected from the group consisting of the miRNAs set forth in rows 1-55 of Table 2.
  • the synthetic lethal RNAi molecule is a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA set forth in rows 1-55 of Table 2.
  • the synthetic lethal RNAi molecule is a pri-miRNA
  • the synthetic lethal RNAi molecule is a pre-miRNA
  • the synthetic lethal RNAi molecule is a miRNA mimic corresponding to a miRNA selected from the group of miRNAs set forth in rows 1-55 of Table 2.
  • the synthetic lethal RNAi molecule is a miRNA selected from the group of miRNAs set forth in rows 1-55 of Table 2, which has a chemical modification or a modified nucleobase.
  • the synthetic lethal RNAi molecule is a nucleic acid encoding a miRNA selected from the group of miRNAs set forth in rows 1-55 of Table 2 or a corresponding pri-miRNA or pre-miRNA thereof.
  • the synthetic lethal RNAi molecule contemplated for use in the treatment of breast cancer in combination with a chemotherapeutic agent is selected from the group consisting of:
  • a miRNA selected from the group consisting of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p;
  • a miRNA comprising an effector sequence of a miRNA at (i);
  • transcript sequence as an effector sequence of a miRNA at (i); (iv) a primary miRNA (pri-miRNA) corresponding to a miRNA of any one of (i) to (iii);
  • the synthetic lethal RNAi molecule is a miRNA selected from the group consisting of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR- 27b-3p.
  • the synthetic lethal RNAi molecule is a miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA selected from the group consisting of miR-199a-5p, miR-29b-2- 5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the synthetic lethal RNAi molecule is a pri-miRNA
  • miRNAs selected from the group consisting of miR-199a-5p, miR- 29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the synthetic lethal RNAi molecule is a pre-miRNA
  • miRNAs selected from the group consisting of miR-199a-5p, miR- 29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the synthetic lethal RNAi molecule is a miRNA mimic corresponding to a miRNA selected from the group consisting of miR-199a-5p, miR- 29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the synthetic lethal RNAi molecule is a miRNA selected from the group consisting of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR- 27b-3p, which has a chemical modification or a modified nucleobase.
  • the synthetic lethal RNAi molecule is a nucleic acid encoding a miRNA selected from miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR- 27b-3p or a corresponding pri-miRNA or pre-miRNA thereof.
  • the synthetic lethal RNAi molecule for use in accordance with the present disclosure is an RNAi molecule corresponding to miR-199a-5p as described in any example hereof.
  • the synthetic lethal RNAi molecule for use in accordance with the present disclosure is an RNAi molecule corresponding to miR-29b-2-5p as described in any example hereof.
  • the synthetic lethal RNAi molecule for use in accordance with the present disclosure is an RNAi molecule corresponding to miR-3151 as described in any example hereof.
  • the synthetic lethal RNAi molecule for use in accordance with the present disclosure is an RNAi molecule corresponding to miR-27a-3p as described in any example hereof.
  • the synthetic lethal RNAi molecule for use in accordance with the present disclosure is an RNAi molecule corresponding to miR-27b-3p as described in any example hereof.
  • the RNAi molecule for use in the method of the disclosure is a miRNA selected from the group of miRNAs set forth in Table 1 or Table 2, or a corresponding pri-miRNA, pre-miRNA thereof or miRNA mimic thereof.
  • the RNAi molecule may be selected from the group of lethal miRNAs set forth in Table 1 or the corresponding pri-miRNA, pre-miRNA or miRNA mimic thereof.
  • the RNAi molecule may be selected from the group of synthetic lethal miRNAs set forth in Table 2 or the corresponding pri-miRNA, pre-miRNA or miRNA mimic thereof.
  • the RNAi molecule may be selected from the group of synthetic lethal miRNAs set forth in rows 1-55 of Table 2 or the
  • the RNAi molecule may be a synthetic lethal RNAi molecule selected from the group consisting of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p or the corresponding pri-miRNA, pre-miRNA or miRNA mimic thereof.
  • the synthetic lethal RNAi molecule is miR-199a-5p or the corresponding pri-miRNA, pre-miRNA or miRNA mimic thereof.
  • the synthetic lethal RNAi molecule is miR-29b-2-5p or the corresponding pri-miRNA, pre-miRNA or miRNA mimic thereof. In one example, the synthetic lethal RNAi molecule is miR-3151or the corresponding pri-miRNA, pre-miRNA or miRNA mimic thereof. In one example, the synthetic lethal RNAi molecule is miR-27a-3p or the corresponding pri-miRNA, pre- miRNA or miRNA mimic thereof. In one example, the synthetic lethal RNAi molecule is miR-27b-3p or the corresponding pri-miRNA, pre-miRNA or miRNA mimic thereof.
  • the RNAi molecule for use in the method of the disclosure is a miRNA, or corresponding pri-miRNA, pre-miRNA or miRNA mimic, comprising an effector sequence of a miRNA set forth in Table 1 or Table 2.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic may comprise an effector sequence of a lethal miRNAs set forth in Table 1.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic may comprise an effector sequence of a synthetic lethal miRNAs set forth in Table 2.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic may comprise an effector sequence of a synthetic lethal miRNAs set forth in rows 1-55 of Table 2.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic may comprise an effector sequence of a synthetic lethal RNAi molecule selected from the group consisting of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic comprises an effector sequence of miR-199a-5p. In one example, the miRNA, pri-miRNA, pre- miRNA or miRNA mimic comprises an effector sequence of miR-29b-2-5p. In one example, the miRNA, pri-miRNA, pre-miRNA or miRNA mimic comprises an effector sequence of miR-3151. In one example, the miRNA, pri-miRNA, pre-miRNA or miRNA mimic comprises an effector sequence of miR-27a-3p. In one example, the miRNA, pri-miRNA, pre-miRNA or miRNA mimic comprises an effector sequence of miR-27b-3p.
  • the RNAi molecule for use in the method of the disclosure is a miRNA, or corresponding pri-miRNA, pre-miRNA or miRNA mimic, comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA set forth in Table 1 or Table 2 or a corresponding pri-miRNA or pri-miRNA thereof.
  • the RNAi molecule may be a miRNA from the same miRNA family as a miRNA set forth in Table 1 or Table 2.
  • miRNA family refers to a group a miRNA species that share identity across at least 6 consecutive nucleotides, also referred to as the "seed sequence", as described in Brennecke et al, (2005) PLoS Biol 3(3):pe85.
  • seed sequence denotes nucleotides at positions 1-6, 1-7, 2-7 or 2-8 of the effector sequence of a miRNA sequence. This is typically located at the 5' end of the miRNA effector sequence.
  • a miRNA, or corresponding pri-miRNA, pre-miRNA, or miRNA mimic comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA set forth in Table 1 or Table 2, will comprise a seed sequence of a miRNA set forth in Table 1 or Table 2.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic may comprise an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a lethal miRNA set forth in Table 1.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic may comprise an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a synthetic lethal miRNA set forth in Table 2.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic may comprise an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a synthetic lethal miRNA set forth in rows 1-55 of Table 2.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic may comprise an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a synthetic lethal RNAi molecule selected from the group consisting of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic comprises an effector sequence which targets the same mRNA transcript sequence as the effector sequence of miR-199a-5p.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic comprises an effector sequence which targets the same mRNA transcript sequence as the effector sequence of miR- 29b-2-5p.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic comprises an effector sequence which targets the same mRNA transcript sequence as the effector sequence of miR-3151.
  • the miRNA, pri-miRNA, pre- miRNA or miRNA mimic comprises an effector sequence which targets the same mRNA transcript sequence as the effector sequence of miR-27a-3p.
  • the miRNA, pri-miRNA, pre-miRNA or miRNA mimic comprises an effector sequence which targets the same mRNA transcript sequence as the effector sequence of miR- 27b-3p.
  • RNAi molecules contemplated for use in the method of the disclosure may be either synthetic or expressed by a suitable vector comprising a DNA template for transcription of the RNAi molecule(s).
  • Synthetic RNAi molecules e.g., miRNAs or precursors thereof and miRNA mimics, may be manufactured by methods known in the art such as by typical oligonucleotide synthesis, and often will incorporate chemical modifications to increase half-life and/or efficacy of the RNAi molecule, and/or to allow for a more robust delivery formulation. Many modifications of oligonucleotides are known in the art.
  • substantially all of the nucleotides of the RNAi molecule of the disclosure are modified. In other examples, all of the nucleotides of the RNAi molecule of the disclosure are modified.
  • RNAi molecules contemplated for use in the method of the disclosure in which "substantially all of the nucleotides are modified" are largely but not wholly modified and can include not more than 5, 4, 3, 2, or 1 unmodified nucleotides.
  • RNAi molecule of the disclosure e.g., a miRNA or corresponding pri-miRNA or pre-miRNA, without disrupting miRNA activity.
  • the RNAi molecule may vary from a corresponding naturally-occurring miRNA sequence, but retain one or more functional characteristics of that miRNA (e.g., enhancement of breast cancer cell susceptibility to chemotherapeutic agents, inhibition of breast cancer cell proliferation, induction of breast cancer cell apoptosis, specific miRNA target inhibition).
  • Such an RNAi molecule may be referred to as a "functional variant" of a naturally-occurring miRNA or corresponding precursor molecule.
  • a functional variant retains all of the functional characteristics of the corresponding naturally-occurring miRNA.
  • an RNAi molecule which is a naturally-occurring miRNA has a nucleobase sequence that is a least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the miRNA or corresponding precursor thereof over a region of about 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more nucleobases, or that the functional variant hybridizes to the complement of the miRNA or precursor thereof under stringent hybridization conditions.
  • the nucleobase sequence of an RNAi molecule which is a functional variant may be capable of hybridizing to one or more target sequences of the miRNA.
  • the or each RNAi molecule contemplated for use in the method of the disclosure comprises one or more overhang regions and/or capping groups at the 3 '-end, 5 '-end, or both ends of one or both strands of the duplex (if provided as a duplex).
  • the overhang can be 1-6 nucleotides in length, for instance 2-6 nucleotides in length, 1-5 nucleotides in length, 2-5 nucleotides in length, 1-4 nucleotides in length, 2- 4 nucleotides in length, 1-3 nucleotides in length, 2-3 nucleotides in length, or 1-2 nucleotides in length.
  • the overhang(s) can be the result of one strand being longer than the other, or the result of two strands of the same length being staggered.
  • the overhang(s) can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be another sequence.
  • the first and second strands can also be joined, e.g., by additional bases to form a hairpin, or by other non- base linkers.
  • the nucleotides in the overhang region(s) of the or each RNA each independently are a modified or unmodified nucleotide including, but no limited to 2'-sugar modified, such as, 2-F, 2'-0-methyl, thymidine (T), deoxy-thymine (dT), 2'- O-methoxyethyl-5-methyluridine (Teo), 2'-0-methoxyethyladenosine (Aeo), 2'-0- methoxyethyl-5-methylcytidine (m5Ceo), and any combinations thereof.
  • dTdT can be an overhang sequence for either end on either strand.
  • the overhang can form a mismatch with the target mRNA or it can be complementary to the gene sequences being targeted or can be another sequence.
  • the 5'- or 3'-overhangs at the strand comprising the effector sequence or the strand comprising the effector complement sequence or both strands of the or each RNAi molecule can be phosphorylated.
  • the overhang region(s) contains two nucleotides having a phosphorothioate between the two nucleotides, where the two nucleotides can be the same or different.
  • the RNAi molecule(s) of the disclosure contain(s) only a single overhang, which can strengthen the interference activity of the RNAi molecule, without affecting its overall stability.
  • the single-stranded overhang is be located at the 3'-terminal end of the effector sequence or, alternatively, at the 3'-terminal end of the effector complement sequence.
  • the RNAi molecule(s) of the disclosure also comprise(s) a blunt end, located at the 5'-end of the effector
  • Modifications include, for example, end modifications, e.g., 5'-end modifications
  • RNAi molecules useful in the method of the disclosure include, but are not limited to RNAi molecules containing modified backbones or no natural internucleoside linkages.
  • RNAi molecules having modified backbones include, among others, those that do not have a phosphorus atom in the backbone.
  • modified RNAi molecules that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.
  • a modified RNAi molecule will have a phosphorus atom in its internucleoside backbone.
  • Representative U.S. patents that teach the preparation of phosphorus -containing linkages include, but are not limited to, U.S. Pat. Nos. 7,015,315; 7,041,816; 7,273,933; 7,321,029; and US Pat RE39464.
  • Modified RNA backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
  • oligonucleosides include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH 2 component parts.
  • Representative U.S. patents that teach exemplary forms of these oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,663,312; 5,633,360; 5,677,437; and 5,677,439.
  • RNAi molecules of the disclosure can also contain one or more substituted sugar moieties.
  • the RNAi molecules described herein can include one of the following at the 2'-position: OH; F; 0-, S-, or N-alkyl; 0-, S-, or N- alkenyl; 0-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl can be substituted or unsubstituted Ci to Cio alkyl or C 2 to Cio alkenyl and alkynyl.
  • Exemplary suitable modifications include 0[(CH 2 ) n O] m CH 3 , 0(CH 2 ) n OCH 3 ,
  • n and m are from 1 to about 10.
  • RNAi molecules useful in the method of the disclosure can also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions.
  • nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
  • Modified nucleobases include other synthetic and natural nucleobases such as deoxy-thymine (dT), 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2- thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4- thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl anal other 8-substituted adenines and guanines, 5-halo, particularly 5-bromo
  • RNAi molecules described herein can also be modified to include one or more locked nucleic acids (LNA).
  • LNA locked nucleic acids
  • a locked nucleic acid is a nucleotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2' and 4' carbons. This structure effectively "locks" the ribose in the 3'- endo structural conformation.
  • the addition of locked nucleic acids to siRNAs has been shown to increase siRNA stability in serum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33 ⁇ ):A 9-AA1).
  • the RNAi molecules of the disclosure e.g., miRNAs and miRNA mimics, to include one or more LNAs to improve serum stability and/or reduce off target effects when treating a subject for breast cancer.
  • RNAi molecules can include N-(acetylaminocaproyl)-4-hydroxyprolinol (Hyp-C6-NHAc), N-(caproyl-4- hydroxyprolinol (Hyp-C6), N-(acetyl-4-hydroxyprolinol (Hyp-NHAc), thymidine-2'-0- deoxythymidine (ether), N-(aminocaproyl)-4-hydroxyprolinol (Hyp-C6-amino), 2- docosanoyl-uridine-3"-phosphate, inverted base dT(idT) and others. Disclosure of this modification can be found in PCT Publication No. WO2011/005861.
  • an RNAi molecule of the disclosure may be provided as a hairpin structure e.g., a pri-miRNA or a pre-miRNA, comprising a stem loop sequence positioned between cognate effector and effector complement sequences such that the RNAi molecule forms a single contiguous sequence.
  • a stem loop sequence should be of sufficient length to permit the effector sequence and the effector complement sequence to anneal to one another. Suitable stem loop sequences may be selected from those known in the art.
  • RNAi molecules used in the method of the disclosure are chemically synthesized.
  • Oligonucleotides e.g., certain modified oligonucleotides or portions of oligonucleotides lacking ribonucleotides
  • Oligonucleotides are synthesized using protocols known in the art, for example as described in Caruthers et al., 1992, Methods in Enzymology 211, 3-19, WO 99/54459, Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684, Wincott et al., 1997, Methods Mol.
  • oligonucleotides makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end, and phosphoramidites at the 3'-end.
  • RNAs without modifications may be synthesized using procedures as described in Usman et al., 1987, J. Am. Chem. Soc, 109, 7845; Scaringe et al., 1990, Nucleic Acids Res., 18, 5433. These syntheses makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end, and phosphoramidites at the 3'-end that can be used for certain RNAi molecules of the disclosure.
  • RNAi molecules used in the method of the disclosure are synthesized, deprotected, and analyzed according to methods described in U.S. Pat. Nos. 6,995,259, 6,686,463, 6,673,918, 6,649,751, and/or 6,989,442.
  • RNAi molecules used in the method of the disclosure are synthesized as discrete components and joined together post- synthetically, for example, by ligation (Moore et al., 1992, Science 256, 9923 or WO 93/23569), or by hybridization following synthesis and/or deprotection.
  • the RNAi molecule contemplated for use in the method of the disclosure is a nucleic acid e.g., a DNA molecule, from which a miRNA, pri- miRNA or pre-miRNA of the disclosure can be transcribed.
  • the method of the disclosure may comprise administering to the subject a nucleic acid so that a miRNA, pri-miRNA or pre-miRNA encoded thereby can be transcribed in the subject.
  • the nucleic acid is DNA. Suitable DNAs from which RNAi molecules of the disclosure may be transcribed are described herein.
  • the nucleic acid contemplated for use in the method of the disclosure may comprise a sequence encoding a pri-miRNA or pre-miRNA corresponding to a miRNA selected from the group of miRNAs set forth in Table 1 or Table 2.
  • the nucleic acid comprises a sequence encoding a pri-miRNA or pre-miRNA corresponding to a miRNA selected from the group of lethal miRNAs set forth in Table 1.
  • the nucleic acid may comprise a sequence encoding a pri- miRNA or pre-miRNA corresponding to a miRNA selected from the group of synthetic lethal miRNAs set forth in Table 2.
  • the nucleic acid may comprise a sequence encoding a pri-miRNA or pre-miRNA corresponding to a miRNA selected from the group of synthetic lethal miRNAs set forth in rows 1-55 of Table 2.
  • the nucleic acid comprises a sequence encoding a pri-miRNA or pre-miRNA corresponding to a synthetic lethal miRNA selected from the group of consisting miR- 199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p. In one example, the nucleic acid comprises a sequence encoding a pri-miRNA or pre-miRNA
  • the nucleic acid comprises a sequence encoding a pri-miRNA or pre-miRNA corresponding to miR-29b-2-5p. In one example, the nucleic acid comprises a sequence encoding a pri-miRNA or pre-miRNA corresponding to miR-3151. In one example, the nucleic acid comprises a sequence encoding a pri-miRNA or pre-miRNA corresponding to miR-27a-3p. In one example, the nucleic acid comprises a sequence encoding a pri-miRNA or pre-miRNA corresponding to miR-27b-3p.
  • the nucleic acid contemplated for use in the method of the disclosure comprises a sequence encoding a pri-miRNA or pre-miRNA corresponding to a miRNA comprising an effector sequence of a miRNA set forth in Table 1 or Table 2.
  • the nucleic acid may comprise a sequence encoding a pri- miRNA or pre-miRNA corresponding to a miRNA comprising an effector sequence of a lethal miRNAs set forth in Table 1.
  • the nucleic acid comprises a sequence encoding a pri-miRNA or pre-miRNA corresponding to a miRNA comprising an effector sequence of a synthetic lethal miRNAs set forth in Table 2.
  • the nucleic acid may comprise a sequence encoding a pri-miRNA or pre-miRNA corresponding to a miRNA comprising an effector sequence of a synthetic lethal miRNAs set forth in rows 1-55 of Table 2.
  • the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence of a synthetic lethal miRNA selected from the group of consisting of miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p.
  • the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence of miR-199a-5p.
  • the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence of miR-29b-2-5p.
  • the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence of miR-3151. In one example, the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence of miR-27a-3p. In one example, the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence of miR-27b-3p.
  • the nucleic acid contemplated for use in the method of the disclosure comprises a sequence encoding a miRNA, pri-miRNA or pri-miRNA, comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a miRNA set forth in Table 1 or Table 2.
  • the nucleic acid may comprise a sequence encoding a miRNA, pri- miRNA or pre-miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a lethal miRNA set forth in Table 1.
  • the nucleic acid may comprise a sequence encoding a miRNA, pri- miRNA or pre-miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a synthetic lethal miRNA set forth in Table 2.
  • the nucleic acid may comprise a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a synthetic lethal miRNA set forth in rows 1-55 of Table 2.
  • the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of a synthetic lethal miRNA selected from the group of consisting of miR-199a-5p, miR-29b-2-5p, miR- 3151, miR-27a-3p, and miR-27b-3p.
  • the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of miR-199a-5p.
  • the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of miR-29b-2-5p. In one example, the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre- miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of miR-3151. In one example, the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of miR-27a-3p. In one example, the nucleic acid comprises a sequence encoding a miRNA, pri-miRNA or pre-miRNA comprising an effector sequence which targets the same mRNA transcript sequence as an effector sequence of miR-27b-3p.
  • a nucleic acid contemplated for use in a method of the disclosure comprises one or more additional elements e.g., to facilitate transcription of the miRNA, pri-miRNA or pre-miRNA encoded thereby.
  • the or each nucleic acid may comprise a promoter operably-linked to a sequence encoding a miRNA, pri-miRNA or pre-miRNA of the disclosure.
  • Other elements e.g.,
  • nucleic acid encoding the RNAi molecule of the disclosure may be linked to a suitable promoter and provided as an expression construct.
  • RNAi molecules of the disclosure to the subject may encode a plurality of the RNAi molecules of the disclosure.
  • the sequences of the nucleic acid encoding the respective RNAi molecules may be operably-linked to the same promoter.
  • the sequences encoding the respective RNAi molecules of the disclosure may be operably-linked to different promoters.
  • nucleic acid encoding the RNAi molecule of the disclosure is provided within a vector, e.g., a plasmid or a miniplasmid or a viral vector. Accordingly, vectors comprising one or more nucleic acid(s) encoding RNAi molecules of the disclosure are contemplated for use in the method of the disclosure. Suitable expression vectors for use in the method of the disclosure are described herein. Accordingly, the present disclosure contemplates the use of an expression vector comprising a nucleic acid encoding an RNAi molecule of the disclosure for treating breast cancer.
  • a nucleic acid encoding an RNAi molecule of the disclosure may be linked to, or in operable linkage with, a promoter for controlling expression of the respective RNAi molecule(s).
  • the promoter is a constitutive promoter.
  • constitutive when made in reference to a promoter means that the promoter is capable of directing transcription of an operably linked nucleic acid sequence in the absence of a specific stimulus (e.g., heat shock, chemicals, light, etc.).
  • constitutive promoters are capable of directing expression of a coding sequence in substantially any cell and any tissue.
  • the promoters used to transcribe the RNAi molecules of the disclosure include a promoter for ubiquitin, CMV, ⁇ -actin, histone H4, EF-la or pgk genes controlled by RNA polymerase II, or promoter elements controlled by RNA polymerase I.
  • a Pol II promoter such as CMV, SV40, Ul, ⁇ -actin or a hybrid Pol II promoter is employed.
  • a promoter controlled by RNA polymerase III is used, such as a U6 promoter (U6-1, U6-8, U6-9), HI promoter, 7SL promoter, a human Y promoter (hYl, hY3, hY4 (see Maraia, et al, Nucleic Acids Res 22(15):3045-52(1994)) and hY5 (see Maraia, et al, Nucleic Acids Res 24(18):3552-59(1994)), a human MRP- 7-2 promoter, an Adenovirus VA1 promoter, a human tRNA promoter, or a 5s ribosomal RNA promoter.
  • U6 promoter U6-1, U6-8, U6-9
  • HI promoter 7SL promoter
  • a human Y promoter hYl, hY3, hY4 (see Maraia, et al, Nucleic Acids Res 22(15):3045-52
  • the promoter is a RNA polIII promoter.
  • the promoter is a U6 promoter.
  • the promoter is a HI promoter.
  • promoters of variable strength are employed.
  • use of two or more strong promoters may tax the cell, by, e.g., depleting the pool of available nucleotides or other cellular components needed for transcription.
  • use of several strong promoters may cause a toxic level of expression of RNAi molecules in the cell.
  • RNAi molecules of the disclosure may be linked to, or in operable linkage with, a plurality of promoters, one or more of those promoters may be weaker than other promoters in the respective expression construct, or all promoters in the construct may express the RNAi molecules at less than a maximum rate.
  • Promoters also may be modified using molecular techniques, or otherwise, e.g., through regulation elements, to attain weaker levels of transcription.
  • Promoters useful in some examples of the present disclosure can be tissue- specific or cell- specific.
  • tissue specific refers to a promoter that is capable of directing selective transcription of a nucleic acid of interest to a specific type of tissue (e.g., breast tissue) in the relative absence of expression of the same nucleotide sequence of interest in a different type of tissue (e.g., liver).
  • cell- specific as applied to a promoter refers to a promoter which is capable of directing selective transcription of a nucleic acid of interest in a specific type of cell in the relative absence of expression of the same nucleotide sequence of interest in a different type of cell within the same tissue.
  • a nucleic acid of the disclosure, or expression vector comprising same may additionally comprise one or more enhancers to increase expression of the or each RNAi molecule.
  • Suitable enhancers will be known to those skilled in the art.
  • a nucleic acid of the disclosure, or expression vector comprising same may comprise a transcriptional terminator linked to the nucleic acid encoding an RNAi molecule of the disclosure.
  • the terminator used will be dependent on the type of promoter employed (e.g., a Pol II- or Pol Ill-type promoter). Suitable terminators will be known to those skilled in the art.
  • the terminators can be different and are matched to the promoter from the gene from which the terminator is derived.
  • Such terminators include the SV40 poly A, the Ad VA1 gene, the 5S ribosomal RNA gene, and the terminators for human t-RNAs.
  • promoters and terminators may be mixed and matched, as is commonly done with RNA pol II promoters and terminators.
  • nucleic acid encoding an RNAi molecule of the disclosure, or the expression vector comprising same can comprise one or more multiple cloning sites and/or unique restriction sites that are located strategically, such that the promoter, RNAi molecule encoding sequence and/or terminator elements are easily removed or replaced.
  • the nucleic acid encoding an RNAi molecule of the disclosure, or the expression vector comprising same can be assembled from smaller oligonucleotide components using strategically located restriction sites and/or complementary sticky ends.
  • the base vector for one approach according to the present disclosure comprises plasmids with a multilinker in which all sites are unique (though this is not an absolute requirement).
  • each promoter is inserted between its designated unique sites resulting in a base cassette with one or more promoters, all of which can have variable orientation.
  • Sequentially, again, annealed primer pairs are inserted into the unique sites downstream of each of the individual promoters, resulting in a single-, double- or multiple-expression cassette construct.
  • the insert can be moved into a suitable expression vector using two unique enzyme sites (the same or different ones) that flank the single-, double- or multiple-expression cassette insert.
  • nucleic acids encoding RNAi molecules useful in the method of the disclosure, or expression constructs and vectors comprising same can be accomplished using any suitable genetic engineering techniques known in the art, including without limitation, the standard techniques of PCR, oligonucleotide synthesis, restriction endonuclease digestion, ligation, transformation, plasmid purification, and DNA sequencing. If the or each nucleic acid encoding an RNAi molecule of the disclosure is to be packaged into a viral particle for delivery to a subject, the or each nucleic acid may comprise or be linked to sequences necessary to package the nucleic acid(s) into viral particles and/or sequences that allow integration of the nucleic acid(s) into the target cell genome.
  • the or each nucleic acid encoding an RNAi molecule of the disclosure may additionally contain or be linked to genes that allow for replication and propagation of virus, however such genes will be supplied in trans. Additionally, the or each nucleic acid encoding an RNAi molecule of the disclosure can contain genes or genetic sequences from the genome of any known organism incorporated in native form or modified. For example, a viral construct may comprise sequences useful for replication of the construct in bacteria.
  • RNAi molecule of the disclosure may also contain or be linked to additional genetic elements.
  • additional genetic elements may include a reporter gene, such as one or more genes for a fluorescent marker protein such as GFP or RFP; an easily assayed enzyme such as beta-galactosidase, luciferase, beta-glucuronidase, chloramphenical acetyl transferase or secreted embryonic alkaline phosphatase; or proteins for which immunoassays are readily available such as hormones or cytokines.
  • genes that may find use in examples of the present disclosure include those coding for proteins which confer a selective growth advantage on cells such as adenosine deaminase, aminoglycodic phosphotransferase, dihydrofolate reductase, hygromycin-B-phosphotransferase, drug resistance, or those genes coding for proteins that provide a biosynthetic capability missing from an auxotroph.
  • a reporter gene is included along with the or each nucleic acid, an internal ribosomal entry site (IRES) sequence can be included.
  • the additional genetic elements are operably linked with and controlled by an independent promoter/enhancer.
  • a suitable origin of replication for propagation of the nucleic acid in bacteria may be employed.
  • the sequence of the origin of replication generally is separated from the nucleic acid encoding an RNAi molecule of the disclosure and other genetic sequences.
  • origins of replication are known in the art and include the pUC, ColEl, 2-micron or SV40 origins of replication.
  • a nucleic encoding an RNAi molecule of the disclosure may be included within an expression vector.
  • the expression vector may be administered to the subject to be treated such that that the RNAi molecule encoded by the nucleic acid is transcribed within the subject.
  • the expression vector is a plasmid, e.g., as is known in the art.
  • the expression vector is mini-circle DNA.
  • Mini-circle DNA is described in U.S. Patent Publication No. 2004/0214329. Mini-circle DNA is useful for persistently high levels of nucleic acid transcription.
  • the circular vectors are
  • mini-circle vectors differ from bacterial plasmid vectors in that they lack an origin of replication, and lack drug selection markers commonly found in bacterial plasmids, e.g. ⁇ -lactamase, tet, and the like. Consequently, minicircle DNA becomes smaller in size, allowing more efficient delivery.
  • the expression vector is a viral vector.
  • a viral vector based on any appropriate virus may be used to deliver a nucleic acid encoding an RNAi molecule of the disclosure.
  • hybrid viral systems may be of use. The choice of viral delivery system will depend on various parameters, such as the tissue targeted for delivery, transduction efficiency of the system, pathogenicity, immunological and toxicity concerns, and the like.
  • Commonly used classes of viral systems used in gene therapy can be categorized into two groups according to whether their genomes integrate into host cellular chromatin (oncoretroviruses and lentiviruses) or persist in the cell nucleus
  • a viral vector of the disclosure integrates into a host cell's chromatin.
  • a viral vector of the disclosure persists in a host cell's nucleus as an extrachomosomal episome.
  • a viral vector is an adenoviral (AdV) vector.
  • Adenoviruses are medium-sized double-stranded, non-enveloped DNA viruses with linear genomes that is between 26-48 Kbp. Adenoviruses gain entry to a target cell by receptor-mediated binding and internalization, penetrating the nucleus in both non-dividing and dividing cells. Adenoviruses are heavily reliant on the host cell for survival and replication and are able to replicate in the nucleus of vertebrate cells using the host's replication machinery.
  • a viral vector is from the Parvoviridae family.
  • the Parvoviridae is a family of small single-stranded, non-enveloped DNA viruses with genomes approximately 5000 nucleotides long. Included among the family members is adeno- associated virus (AAV).
  • AAV adeno- associated virus
  • a viral vector of the disclosure is an AAV.
  • AAV is a dependent parvovirus that generally requires co-infection with another virus (typically an adenovirus or herpesvirus) to initiate and sustain a productive infectious cycle. In the absence of such a helper virus, AAV is still competent to infect or transduce a target cell by receptor-mediated binding and internalization, penetrating the nucleus in both non-dividing and dividing cells.
  • progeny virus is not produced from AAV infection in the absence of helper virus, the extent of transduction is restricted only to the initial cells that are infected with the virus. It is this feature which makes AAV a desirable vector for the present disclosure.
  • AAV appears to lack human pathogenicity and toxicity (Kay, et ah, Nature. 424: 251 (2003)). Since the genome normally encodes only two genes it is not surprising that, as a delivery vehicle, AAV is limited by a packaging capacity of 4.5 single stranded kilobases (kb). However, although this size restriction may limit the genes that can be delivered for replacement gene therapies, it does not adversely affect the packaging and expression of shorter sequences, such as pre-miRNAs and pri-miRNAs.
  • Retroviruses comprise single- stranded RNA animal viruses that are characterized by two unique features. First, the genome of a retrovirus is diploid, consisting of two copies of the RNA. Second, this RNA is transcribed by the virion- associated enzyme reverse transcriptase into double-stranded DNA. This double- stranded DNA or provirus can then integrate into the host genome and be passed from parent cell to progeny cells as a stably-integrated component of the host genome.
  • a viral vector is a lentivirus.
  • Lentivirus vectors are often pseudotyped with vesicular steatites virus glycoprotein (VSV-G), and have been derived from the human immunodeficiency virus (HIV); visan-maedi, which causes encephalitis (visna) or pneumonia in sheep; equine infectious anemia virus (EIAV), which causes autoimmune hemolytic anemia and encephalopathy in horses; feline immunodeficiency virus (FIV), which causes immune deficiency in cats; bovine immunodeficiency virus (BIV) which causes lymphadenopathy and lymphocytosis in cattle; and simian immunodeficiency virus (SIV), which causes immune deficiency and encephalopathy in non-human primates.
  • VSV-G vesicular steatites virus glycoprotein
  • Vectors that are based on HIV generally retain ⁇ 5% of the parental genome, and ⁇ 25% of the genome is incorporated into packaging constructs, which minimizes the possibility of the generation of reverting replication- competent HIV.
  • Biosafety has been further increased by the development of self- inactivating vectors that contain deletions of the regulatory elements in the downstream long-terminal-repeat sequence, eliminating transcription of the packaging signal that is required for vector mobilization.
  • the main advantage to the use of lentiviral vectors is that gene transfer is persistent in most tissues or cell types.
  • a lentiviral-based construct used to express a RNA of the disclosure comprises sequences from the 5' and 3' long terminal repeats (LTRs) of a lentivirus.
  • the viral construct comprises an inactivated or self-inactivating 3' LTR from a lentivirus.
  • the 3' LTR may be made self-inactivating by any method known in the art.
  • the U3 element of the 3' LTR contains a deletion of its enhancer sequence, e.g., the TATA box, Spl and NF-kappa B sites.
  • the provirus that is integrated into the host genome will comprise an inactivated 5' LTR.
  • the LTR sequences may be LTR sequences from any lentivirus from any species.
  • the lentiviral-based construct also may incorporate sequences for MMLV or MSCV, RSV or mammalian genes.
  • the U3 sequence from the lentiviral 5' LTR may be replaced with a promoter sequence in the viral construct. This may increase the titer of virus recovered from the packaging cell line.
  • An enhancer sequence may also be included.
  • RNAi molecule of the present invention may be delivered to cells of interest, including but not limited to gene-deleted adenovirus-transposon vectors (see Yant, et ah, Nature Biotech. 20:999-1004 (2002)); systems derived from Sindbis virus or Semliki forest virus (see Perri, et al, J. Virol. 74(20):9802-07 (2002)); systems derived from
  • Newcastle disease virus or Sendai virus.
  • RNAi molecules which are suitable for use in the method of the disclosure will preferably be capable of reducing viability of a breast cancer cell e.g., by conferring a lethal phenotype to the cell, when administered alone or in combination with a chemotherapeutic agent. Accordingly, one or more functional assays may be performed to determine the ability of the RNAi molecule to affect viability and/or confer a lethal or synthetic lethal phenotype to breast cancer cells. Suitable functional assays are described in Examples 1, 2 and 4 hereof.
  • Exemplary cell lines useful as cell culture models for breast cancer are the MDA- MB-231, MDA-MB-468, SKBR3, and BT-474 cell lines described in Example 1, and the MDA-MB-436, HS578T, and HCC70 cell lines described in Example 2.
  • assays performed in MDA-MB-231, MDA-MB-468, MDA-MB-436, HS578T, and HCC70 cell lines may be particularly useful to determining the ability of an RNAi molecule to affect viability and/or confer a lethal or synthetic lethal phenotype to a TNBC subtype cell or cell mass.
  • assays performed in SKBR3 cells may be particularly useful to determining the ability of an RNAi molecule to affect viability and/or confer a lethal or synthetic lethal phenotype to a Her2 positive subtype breast cancer cell or cell mass.
  • assays performed in BT-474 cells may be particularly useful to determining the ability of an RNAi molecule to affect viability and/or confer a lethal or synthetic lethal phenotype to a Luminal B subtype breast cancer cell or cell mass.
  • RNAi molecule of the disclosure activity of an RNAi molecule of the disclosure is determined by administering the RNAi molecule to the cell and subsequently assaying viability of the cell using a CellTiter-Glo luminescent assay.
  • An RNAi molecule which is able to reduce breast cancer cell viability by at least 50% may be considered a "lethal" RNAi molecule and useful in the method of the disclosure e.g., as a standalone or combination therapy.
  • an RNAi molecule as an adjunctive agent for treatment of breast cancer may be evaluated.
  • the activity of an RNAi molecule may be determined by administering the RNAi molecule to the breast cancer cell in combination with a chemo therapeutic agent e.g., a low dose IC20 of epirubicin or docetaxel (or other chemotherapeutic known to be useful for treatment of breast cancer as described herein).
  • a chemo therapeutic agent e.g., a low dose IC20 of epirubicin or docetaxel (or other chemotherapeutic known to be useful for treatment of breast cancer as described herein).
  • Cell viability may then be determined using a CellTiter-Glo luminescent assay.
  • RNAi molecule which decreases cell viability by less than 30% when administered alone, but which, when administered with a sub-lethal dose of chemotherapy (IC20), decreases cell viability by more than 50% relative to cells recieving the IC20 of chemotherapy alone, may be considered a "synthetic lethal" RNAi molecule and useful in the combination treatment method of the disclosure.
  • RNAi molecules of the disclosure are described and reviewed in Rashid OM and Takabe K (2015) Expert Opinion on Drug Metabolism & Toxicology l l(2):221-230, the entire contents of which is incorporated herein by reference.
  • animal models which may be useful for studying breast cancer and, in particular, for assaying RNAi molecules of the disclosure include Xenografts of MDA-MB-231 and/or MDA- MB-468 human breast cancer cells into immunodeficient hosts e.g., mice.
  • Other examples include xenografts of primary patient-derived breast cancer cells into immunodeficient hosts e.g., mice, and allografts of murine 4T1 cells into immune competent hosts e.g., mice.
  • RNAi molecules of the disclosure may be incorporated into a pharmaceutical composition. Accordingly, the present disclosure also provides a pharmaceutical composition comprising any one or more RNAi molecule, a nucleic acid or an expression vector described herein. It is contemplated that the
  • composition may be used in a method of treating breast cancer as described herein.
  • a pharmaceutical composition of the disclosure will preferably comprise a therapeutically effective amount of the RNAi molecule or a nucleic acid or expression vector encoding same, for treating breast cancer.
  • a "therapeutically effective amount” is at least the minimum concentration or amount required to effect a measurable improvement of the breast cancer.
  • a therapeutically effective amount herein may vary according to factors such as the disease state, age, sex, and weight of the patient, and the ability of the RNAi molecule, nucleic acid, or expression vector to elicit a desired response in the individual.
  • a therapeutically effective amount is also one in which any toxic or detrimental effects of the RNAi molecule, or nucleic acid or expression vector encoding same, are outweighed by the therapeutically beneficial effects.
  • the pharmaceutical composition of the disclosure may also comprise one or more pharmaceutically-acceptable carriers, excipients or diluents.
  • Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985).
  • the choice of pharmaceutical carrier, excipient or diluent may be selected with regard to the intended route of administration and standard
  • the carrier included in the pharmaceutical composition may be suited for delivery of the RNAi molecule, nucleic acid or expression vector of the disclosure to neural crest-derived tissue of a subject following administration of the composition thereto.
  • an RNAi molecule described herein may be formulated for delivery using the "EnGeneIC Delivery Vehicle” (EDV) system developed by EnGeneIC Molecular Delivery Pty Ltd (Sydney), which is based on the use of intact, bacterially derived minicells.
  • EDV EnGeneIC Delivery Vehicle
  • the EDVTM system is described, for example, in published international applications WO2006/021894 and WO2009/027830, the respective contents of which are incorporated here by reference.
  • a pharmaceutical composition of the disclosure may comprise the one or more RNAi molecules, nucleic acids or expression vectors as described herein loaded into EDVs i.e., intact minicells.
  • Minicells which are useful for delivery of the RNAi molecules of the disclosure and which may be provided in the pharmaceutical compositions described herein are typically anucleate forms of E. coli or other bacterial cells, engendered by a disturbance in the coordination, during binary fission, of cell division with DNA segregation.
  • Prokaryotic chromosomal replication is linked to normal binary fission, which involves mid-cell septum formation.
  • mutation of min genes such as minCD
  • minCD can remove the inhibition of septum formation at the cell poles during cell division, resulting in production of a normal daughter cell and an anucleate minicell.
  • Minicells are distinct from other small vesicles that are generated and released spontaneously in certain situations and, in contrast to minicells, are not due to specific genetic rearrangements or episomal gene expression. In the present disclosure, it is desirable for minicells to have intact cell walls ("intact minicells").
  • anucleate minicells also are generated following a range of other genetic rearrangements or mutations that affect septum formation, for example in the JMVB 1 in B. subtilis.
  • Minicells also can be formed following a perturbation in the levels of gene expression of proteins involved in cell division/chromosome segregation. For example, overexpression of minE leads to polar division and production of minicells.
  • chromosome-less minicells may result from defects in chromosome segregation for example the smc mutation in Bacillus subtilis, spoOJ deletion in B. subtilis, mukB mutation in E. coli, and parC mutation in E. coli. Gene products may be supplied in trans.
  • Caf A When over-expressed from a high- copy number plasmid, for example, Caf A may enhance the rate of cell division and/or inhibit chromosome partitioning after replication, resulting in formation of chained cells and anucleate minicells.
  • Minicells can be prepared from any bacterial cell of Gram-positive or Gram-negative origin.
  • RNAi molecules, nucleic acid and expression vectors described herein may therefore be packaged directly into intact minicells. This process bypasses the previously required steps of, for example, cloning nucleic acids encoding functional nucleic acid into expression plasmids, transforming minicell -producing parent bacteria with the plasmids and generating recombinant minicells. Instead, plasmid-free nucleic acid molecules can be packaged directly into intact minicells by co-incubating a plurality of intact minicells with RNAi molecules, nucleic acids or expression vectors described herein in a buffer. In some embodiments, the co-incubation may involve gentle shaking, while in others the co-incubation is static.
  • the buffer comprises buffered saline, for example a IX phosphate buffer solution.
  • the buffered saline can be in gelatin form.
  • the co-incubation is conducted at a temperature of about 4°C to about 37°C; about 20°C to about 30°C; about 25°C; or about 37°C.
  • the co- incubation can comprise about 10 7', 108°, 109', 1010 , 1011, 101 1 2" or 101 1 3 J minicells. Specific parameters of temperature, time, buffer, minicell concentration, etc. can be optimized for a particular combination of conditions.
  • RNAi molecules, nucleic acid and expression vectors of the disclosure remain inside the minicell and are protected from degradation.
  • prolonged incubation studies with siRNA-packaged minicells incubated in sterile saline showed no leakage of siRNAs.
  • co-incubating siRNA-packaged minicells with nucleases confirmed that the siRNAs had penetrated the outer membrane of the intact minicells and were protected from degradation.
  • packaged siRNA are stable in the minicell cytoplasm.
  • Packaged siRNA also avoid the degradative machinery present within phagolysosomes, such as acids, free oxygen radicals and acid hydrolases (Conner and Schmid, 2003), to effect target mRNA knockdown within the mammalian cell. Thus, this approach is particularly useful with the RNAi molecules of the disclosure.
  • RNAi molecules, nucleic acid and expression vectors described herein directed to different mRNA targets can be packaged in the same minicell.
  • Such an approach can be used to combat drug resistance and apoptosis resistance.
  • cancer patients including those suffering from breast cancer, routinely exhibit resistance to chemotherapeutic drugs.
  • resistance can be mediated by over-expression of genes such as multi-drug resistance (MDR) pumps and anti- apoptotic genes, among others.
  • minicells can be packaged with therapeutically significant concentrations of RNAi molecules, nucleic acid and expression vectors of the disclosure and administered to a patient before, during or after chemotherapy.
  • packaging into the same minicell multiple RNAi molecules, nucleic acid and expression vectors described herein directed to different mRNA targets can enhance therapeutic success since most molecular targets are subject to mutations and have multiple alleles.
  • the carrier is a lipid-based carrier, cationic lipid, or liposome nucleic acid complex, a liposome, a micelle, a virosome, a lipid nanoparticle or a mixture thereof.
  • the carrier is a biodegradable polymer-based carrier, such that a cationic polymer-nucleic acid complex is formed.
  • the carrier may be a cationic polymer microparticle suitable for delivery of an RNAi molecule, nucleic acid or expression vector of the disclosure to a breast cancer cell.
  • cationic polymers for delivery compositions to cells is known in the art, such as described in Judge et al. Nature 25: 457-462 (2005), the contents of which is incorporated herein by reference.
  • An exemplary cationic polymer-based carrier is a cationic DNA binding polymer, such as polyethylenimine.
  • cationic polymers suitable for complexing with, and delivery of, RNAi molecules, nucleic acids and expression vectors of the disclosure include poly(L-lysine) (PLL), chitosan, PAMAM dendrimers, and poly(2- dimethylamino)ethyl methacrylate (pDMAEMA). These are other suitable cationic polymers are known in the art and are described in Mastrobattista and Hennink, Nature Materials, 11: 10-12 (2012), WO/2003/097107 and WO/2006/041617, the full contents of which are incorporated herein by reference. Such carrier formulations have been developed for various delivery routes including parenteral subcutaneous injection, intravenous injection and inhalation.
  • the carrier is DOTAP and/or some other cationic lipid- mediated nucleic acid delivery system.
  • DOTAP has been used for the systemic delivery of a siRNA for gene slicing, e.g., Sorenson et al, J. Mol. Biol. 327:761-766 (2003), the entire contents of which is incorporated herein by reference.
  • the carrier is a cyclodextrin-based carrier such as a cyclodextrin polymer-nucleic acid complex.
  • the carrier is a protein-based carrier such as a cationic peptide-nucleic acid complex.
  • the carrier is a lipid nanoparticle.
  • Exemplary nanoparticles are described, for example, in US7514099.
  • an RNAi molecule, nucleic acid or expression vector of the disclosure is formulated with a lipid nanoparticle composition comprising a cationic lipid/Cholesterol/PEG-C-DMA/DSPC (e.g., in a 40/48/2/10 ratio), a cationic lipid/Cholesterol/PEG-DMG/DSPC (e.g., in a 40/48/2/10 ratio), or a cationic lipid/Cholesterol/PEG-DMG (e.g., in a 60/38/2 ratio).
  • the cationic lipid is Octyl CL in DMA, DL in DMA, L-278, DLinKC2DMA, or MC3.
  • an RNAi molecule, nucleic acid or expression vector of the disclosure is formulated with any of the cationic lipid formulations described in WO 2010/021865; WO 2010/080724; WO 2010/042877; WO 2010/105209 or WO
  • an RNAi molecule, nucleic acid or expression vector of the disclosure is conjugated to or complexed with another compound, e.g., to facilitate delivery of the RNAi molecule, nucleic acid or expression vector.
  • conjugates are described in US 2008/0152661 and US 2004/0162260 (e.g., CDM-LBA, CDM-Pip-LBA, CDM-PEG, CDM-NAG, etc.).
  • polyethylene glycol is covalently attached to an RNAi molecule, nucleic acid or expression vector of the disclosure.
  • the attached PEG can be any molecular weight, e.g., from about 100 to about 50,000 daltons (Da).
  • an RNAi molecule, nucleic acid or expression vector of the disclosure is formulated with a carrier comprising surface-modified liposomes containing poly(ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes), such as is disclosed in for example, WO 96/10391; WO
  • an RNAi molecule, nucleic acid or expression vector of the disclosure can also be formulated or complexed with polyethyleneimine or a derivative thereof, such as polyethyleneimine -polyethyleneglycol-N-acetylgalactosamine (PEI- PEG-GAL) or polyethyleneimine-polyethyleneglycol-tri-N-acetylgalactosamine (PEI- PEG-triGAL) derivatives.
  • PEI- PEG-GAL polyethyleneimine-polyethyleneglycol-N-acetylgalactosamine
  • PEI- PEG-triGAL polyethyleneimine-polyethyleneglycol-tri-N-acetylgalactosamine
  • RNAi molecule, nucleic acid or expression vector of the disclosure is complexed with membrane disruptive agents such as those described in U.S. Patent Application Publication No. 2001/0007666.
  • cyclodextrins see for example, Gonzalez et al., 1999, Bioconjugate Chem., 10, 1068-1074; or WO 03/46185
  • PLGA poly(lactic-co-glycolic)acid
  • PLCA microspheres see for example US 2002130430.
  • RNAi molecules of the disclosure have been shown to be particularly useful in treating breast cancer when administered in combination with a chemotherapeutic agent e.g., at low dose IC20. It therefore follows that a pharmaceutical composition of the disclosure may comprise, or be packaged together with, one or more chemotherapeutic agents approved for treatment of breast cancer. Accordingly, the present disclosure provides a pharmaceutical composition comprising an RNAi molecule, nucleic acid or expression vector of the disclosure and a
  • the RNAi molecule, nucleic acid or expression vector which is formulated or packaged together with the chemotherapeutic agent corresponds to a lethal RNAi molecule described herein e.g., as described in Table 1.
  • the RNAi molecule, nucleic acid or expression vector which is formulated or packaged together with the chemotherapeutic agent corresponds to a synthetic lethal RNAi molecule described herein e.g., as described in Table 2.
  • synthetic lethal RNAi molecules of the disclosure are those that have been shown reduce breast cancer cell viability when administered in combination with a chemotherapeutic agent.
  • the chemotherapeutic agent may be selected from a vinca alkaloid, a taxane, a platinum-based agent, or an anthracycline.
  • the chemotherapeutic agent is a vinca alkaloid e.g., vincristine, vinblastine, vinorelbine or vindesine.
  • the chemotherapeutic agent is a taxane e.g., paclitaxel, docetaxel and cabazitaxel.
  • the chemotherapeutic agent is a platinum-based agent e.g., cisplatin, carboplatin, oxaliplatin or nedaplatin.
  • the chemotherapeutic agent is an anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • Other suitable chemotherapeutic drugs for treatment of breast cancer will be known in the art.
  • a pharmaceutical composition of the disclosure may desirably include materials that increase the biological stability of the RNAi molecule, nucleic acid or expression vector of the disclosure and/or materials that increase the ability of the compositions to localise to breast cancer cells and/or target breast cancer cells selectively.
  • the pharmaceutical compositions of the disclosure may be administered in
  • pharmaceutically acceptable carriers e.g., physiological saline
  • pharmaceutically acceptable carriers e.g., physiological saline
  • One having ordinary skill in the art can readily formulate a pharmaceutical composition that comprises an RNAi molecule, nucleic acid or expression vector of the disclosure.
  • an isotonic formulation is used.
  • additives for isotonicity can include sodium chloride, dextrose, mannitol, sorbitol and lactose.
  • isotonic solutions such as phosphate buffered saline are preferred.
  • Stabilizers include gelatin and albumin.
  • a vasoconstriction agent is added to the formulation.
  • the compositions according to the present disclosure are provided sterile and pyrogen free. Suitable pharmaceutical carriers, as well as pharmaceutical necessities for use in pharmaceutical formulations, are described in Remington: The Science and Practice of Pharmacy (formerly Remington's).
  • compositions of the disclosure can also comprise conventional pharmaceutical excipients and/or additives.
  • suitable pharmaceutical excipients include stabilizers, antioxidants, osmolality adjusting agents, buffers, and pH adjusting agents.
  • Suitable additives include, e.g., physiologically biocompatible buffers (e.g.,
  • tromethamine hydrochloride additions of chelants (e.g., DTPA or DTPA-bisamide) or calcium chelate complexes (e.g., calcium DTPA, CaNaDTPA-bisamide), or, optionally, additions of calcium or sodium salts (e.g., calcium chloride, calcium ascorbate, calcium gluconate or calcium lactate).
  • chelants e.g., DTPA or DTPA-bisamide
  • calcium chelate complexes e.g., calcium DTPA, CaNaDTPA-bisamide
  • calcium or sodium salts e.g., calcium chloride, calcium ascorbate, calcium gluconate or calcium lactate.
  • the pharmaceutical composition of the disclosure may be conveniently formulated according to the desired route of administration to a subject.
  • Routes of administration include, but are not limited to, intramuscular, intraperitoneal, intradermal, subcutaneous, intravenous, intraarterially, intraoccularly and oral as well as transdermal or by inhalation or suppository.
  • Exemplary routes of administration include intravenous, intramuscular, oral, intraperitoneal, intradermal, intraarterial and subcutaneous injection.
  • the pharmaceutical composition of the disclosure is formulated for intravenous administration.
  • compositions are useful for pharmaceutical applications and may readily be formulated in a suitable sterile, non-pyrogenic vehicle, e.g., buffered saline for injection, for parenteral administration e.g., intravenously (including intravenous infusion), EVI, SC, and for intraperitoneal administration.
  • a suitable sterile, non-pyrogenic vehicle e.g., buffered saline for injection
  • parenteral administration e.g., intravenously (including intravenous infusion), EVI, SC, and for intraperitoneal administration.
  • the volume, concentration, and formulation of the pharmaceutical composition as well as the dosage regimen may be tailored specifically to maximize cellular delivery while minimizing toxicity such as an inflammatory response e.g, relatively large volumes (5, 10, 20, 50 ml or more) with corresponding low concentrations of active ingredients, as well as the inclusion of an anti-inflammatory compound such as a corticosteroid, may be utilized if desired.
  • an inflammatory response e.g, relatively large volumes (5, 10, 20, 50 ml or more) with corresponding low concentrations of active ingredients, as well as the inclusion of an anti-inflammatory compound such as a corticosteroid, may be utilized if desired.
  • an RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used to treat breast cancer, either as a standalone treatment or as an adjunct to chemotherapy.
  • the present disclosure provides methods for treating breast cancer by administering to a subject suffering therefrom an RNAi molecule, a nucleic acid, an expression vector or a pharmaceutical composition of the disclosure.
  • the breast cancer to be treated may be refractory to treatment with the
  • chemotherapeutic agent e.g., in the absence of adjunctive treatment with the RNAi molecule, a nucleic acid or an expression vector of the disclosure.
  • RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used to treat breast cancer in conjunction with surgical treatment e.g., breast-conserving surgery, mastectomy or surgery to remove lymph nodes.
  • RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used to treat breast cancer which is non-resectable, either as a standalone treatment or as an adjunct to chemotherapy or radiotherapy.
  • the breast cancer to be treated may be any breast cancer subtype, such as a TNBC subtype breast cancer, a HER2 type breast cancer, a Luminal A subtype breast cancer or a Luminal B subtype breast cancer.
  • RNAi molecules, nucleic acids, expression vectors or pharmaceutical compositions of the disclosure can be administered to a subject by any means suitable for delivery of the RNAi molecule(s), nucleic acid(s) or expression vector(s) to breast cancer cells of the subject.
  • the RNAi molecules of the disclosure when the RNAi molecules of the disclosure is a miRNA or a corresponding precursor molecule or miRNA mimic as described herein, the RNAi molecule can be administered by any methods suitable to transfect cells of the subject with the RNAi molecule.
  • the RNAi molecule is a nucleic acid encoding a miRNA or corresponding precursor molecule of the disclosure
  • the nucleic acid or expression vector comprising same may be transfected or transduced into the cells of a subject.
  • a subject to be treated may be transfected with a plasmid, or transduced with a viral vector, comprising one or more nucleic acids encoding one or more RNAi molecules of the disclosure.
  • an RNAi molecule described herein e.g., miRNA or miRNA mimic
  • an RNAi molecule described herein may be delivered via the "EnGeneIC Delivery Vehicle” system developed by EnGeneIC Molecular Delivery Pty Ltd (Sydney), which is based on the use of intact, bacterially derived minicells.
  • the EDVTM system is described, for example, in published international applications WO2006/021894 and WO2009/027830, the respective contents of which are incorporated here by reference.
  • the RNAi molecule(s) described here are delivered using intact, bacterially derived minicells. These minicells are delivered specifically to target tissues, using bispecific antibodies. One arm of such an antibody has specificity for the target tissue, while the other has specificity for the minicell. The antibody brings minicells to the target cell surface, and then the minicells are brought into the cell by endocytosis. After uptake into the tumour cell there is a release of the minicell contents, i.e., the RNAi molecule of the disclosure.
  • specificity against any cell surface marker for breast cancer e.g., CD44, CD133, epithelial surface antigen (ESA) or CD24, could be used in accordance with the disclosure.
  • ESA epithelial surface antigen
  • RNAi molecules, nucleic acids, expression vectors and compositions of the disclosure can be administered by a number of routes including, but not limited to intramuscular, intraperitoneal, intradermal, subcutaneous, intravenous, intraarterially, intraoccularly, intrapleural, and oral as well as transdermal or by inhalation or suppository.
  • RNAi molecules, nucleic acids, and expression vectors of the disclosure can also be administered via liposomes or nanoparticles i.e., which are present in a composition of the disclosure.
  • Such administration routes and appropriate formulations are described herein and generally known to those of skill in the art.
  • Administration of the formulations described herein may be accomplished by any acceptable method that allows the RNAi molecule, nucleic acid or expression vector of the disclosure to reach its target. The particular mode selected will depend of course, upon exemplary factors such as the particular formulation, the severity of the state of the subject being treated, and the dosage required for therapeutic efficacy.
  • Other delivery systems suitable include but are not limited to time-release, delayed release, sustained release, or controlled release delivery systems. Such systems may avoid repeated administrations in many cases, increasing convenience to the subject and the physician.
  • Many types of release delivery systems are available and known to those of ordinary skill in the art. They include, for example, polymer -based systems such as polylactic and/or polyglycolic acids, polyanhydrides, polycaprolactones, copolyoxalates, polyesteramides, polyorthoesters, polyhydroxybutyric acid, and/or combinations of these.
  • Dosages for treating a particular subject for breast cancer can be determined by one of ordinary skill in the art using conventional considerations, (e.g., by means of an appropriate, conventional pharmacological protocol).
  • a physician may, for example, prescribe a relatively low dose at first, subsequently increasing the dose until an appropriate response is obtained.
  • the dose administered to a subject is sufficient to effect a beneficial therapeutic response in the subject over time, or, e.g., to reduce symptoms, or other appropriate activity, depending on the application.
  • the dose is determined by the efficacy of the particular formulation, and the activity, stability or serum half-life of the RNAi molecule employed and the condition of the subject, as well as the body weight or surface area of the subject to be treated.
  • a dosage of the RNAi molecule, nucleic acid, expression vector or composition comprising same for use in the method of the disclosure will be sufficient to reduce viability of a breast cancer cell in the subject e.g., by at least 50%.
  • the dosage suitable for use in the method of the disclosure is preferably one that avoids or minimises undue adverse side effects.
  • Adverse side effects may include but are not limited to nausea, vomiting, toxicity, irritation, allergic response, and death.
  • An adverse side effects may be "undue" when the risk outweighs the benefit provided by an RNAi molecule described herein.
  • the size of the dose is also determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a particular vector, and formulation, in a particular subject.
  • RNAi molecules of the disclosure have been shown to be particularly useful in treating breast cancer when administered in combination with a chemotherapeutic agent e.g., at low dose IC20. It therefore follows that the RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used as an adjunct to conventional chemotherapy approved for treatment of breast cancer. It is contemplated that synthetic lethal RNAi molecules of the disclosure e.g., such as those related to the miRNAs in Table 2 herein, may be particularly suited for combination therapy, as these RNAi molecules were identified based on the criteria that they reduce breast cancer cell viability in the presence of a chemotherapeutic agent, but not on their own. Naturally, it will be appreciated by a person skilled on the art that lethal RNAi molecules of the disclosure e.g., such as those related to the miRNAs in Table 1 herein, may also be efficacious in combination therapy.
  • an RNAi molecule, nucleic acid, expression vector or composition described herein may be administered to a subject suffering from breast cancer in order to reduce a therapeutically effective dose of a chemotherapeutic agent which is effective for treating the breast cancer i.e., relative to a dose of the chemotherapeutic agent which is therapeutically effective in a subject who has not or will not be administered an RNAi molecule, nucleic acid, expression vector or composition of the disclosure.
  • the reduced dose of the chemotherapeutic agent may be a IC30 concentration of the chemotherapeutic agent.
  • the reduced dose of the chemotherapeutic agent may be a IC20 concentration of the chemotherapeutic agent.
  • the reduced dose of the chemotherapeutic agent may be a IC10 concentration of the chemotherapeutic agent.
  • RNAi molecule, nucleic acid, expression vector or composition described herein may be used to improve efficacy of a
  • RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used to improve efficacy of a chemotherapeutic agent to treat breast cancer in a subject who would otherwise be refractory to treatment with the chemotherapeutic agent in the absence of receiving the RNAi molecule, nucleic acid, expression vector or composition of the disclosure.
  • an RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used to improve efficacy of a chemotherapeutic agent to treat breast cancer in a subject who has previously entered remission and relapsed i.e., suffering from recurrent breast cancer.
  • an RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used to improve efficacy of a chemotherapeutic agent to treat breast cancer which has metastasized.
  • RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used to treat breast cancer in
  • RNAi molecule, nucleic acid, expression vector or composition of the disclosure may be used to treat breast cancer which is non-resectable, either as a standalone treatment or as an adjunct to
  • the combination therapy method of the disclosure comprises administering an RNAi molecule, nucleic acid, expression vector or composition described herein to a subject with breast cancer who has previously received chemotherapy.
  • the RNAi molecule, nucleic acid, expression vector or composition described herein is used as a pre-treatment for a subject suffering from breast cancer and is administered prior to administration of a chemotherapeutic agent.
  • the administration of an RNAi molecule, nucleic acid, expression vector or composition described herein may therefore precede and/or follow administration of a chemotherapeutic agent e.g., by intervals ranging from minutes to weeks.
  • an RNAi molecule, nucleic acid, expression vector or composition described herein is used as an adjunctive treatment for a patient suffering from breast cancer and is administered at substantially the same time as a chemotherapeutic agent or together.
  • the combination therapy method may further comprise actively administering to the subject the chemotherapeutic agent.
  • the chemotherapeutic agent and the RNAi molecule, nucleic acid, expression vector or composition described herein are administered together e.g., in the same composition.
  • the chemotherapeutic agent and the RNAi molecule, nucleic acid, expression vector or composition described herein are administered concurrently e.g., as separate compositions.
  • the chemotherapeutic agent and the RNAi molecule, nucleic acid, expression vector or composition described herein are administered sequentially.
  • RNAi molecules, nucleic acid, expression vector or composition described herein are administered separately to the subject, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the chemotherapeutic agent and the RNAi molecule, nucleic acid, expression vector or composition would still be able to exert an advantageously combined effect on the breast cancer cell.
  • the chemotherapeutic agent may be selected from a vinca alkaloid, a taxane, a platinum-based agent, or an anthracycline.
  • the chemotherapeutic agent is a vinca alkaloid e.g., vincristine, vinblastine, vinorelbine or vindesine.
  • the chemotherapeutic agent is a taxane e.g., paclitaxel, docetaxel and cabazitaxel.
  • the chemotherapeutic agent is a platinum-based agent e.g., cisplatin, carboplatin, oxaliplatin or nedaplatin.
  • the chemotherapeutic agent is an anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • anthracycline e.g., daunorubicin, doxorubicin, epirubicin, idarubicin or mitoxantrone.
  • Other suitable chemotherapeutic drugs for treatment of breast cancer will be known in the art.
  • RNAi molecule, nucleic acid, expression vector or composition of the disclosure which would be required to treat a subject suffering from breast cancer in combination therapy.
  • the therapeutically effective dose level for any particular patient will depend upon a variety of factors including: the type and severity of breast cancer to be treated; activity or dose of any adjunctive agents e.g., the chemotherapeutic agent; the composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration; the route of
  • RNAi molecule nucleic acid, expression vector or composition of the disclosure
  • duration of the treatment the type of chemotherapeutic drugs used in combination or coincidental with the treatment, together with other related factors well known in medicine.
  • the present disclosure also provides an RNAi molecule, nucleic acid, expression vector or composition of the disclosure in a kit.
  • the kit may comprise one or more containers.
  • the kit typically contains an RNAi molecule, nucleic acid, expression vector or composition of the disclosure with instructions for its administration e.g., in a method of the disclosure.
  • the kit contains a first container comprising an RNAi molecule, nucleic acid, expression vector or composition of the disclosure and second container comprising chemotherapeutic agent, such as a vinca alkaloid, taxane, platinum-based drug or an anthracycline.
  • the kit is intended for treatment of breast cancer in accordance with a method of treatment described herein. Examples
  • Example 1 Genome-wide functional microRNA screen in breast cancer
  • the inventors performed an unbiased functional synthetic lethal screen of available microRNAs in breast cancer cells to identify those microRNAs that either kill breast cancer cells on their own, or which sensitise breast cancer cells to chemotherapeutic agents used as standard of care in the treatment of breast cancer.
  • MDA-MB-231 MDA-MB-468
  • SKBR3 human epidermal growth factor 2
  • BT-474 Luminal B (Lum B) breast cancer cell line i.e., positive for estrogen receptor (ER).
  • All breast cancer cell lines were obtained from American Type Culture Collection (ATCC). The breast cancer cell lines were cultivated in RPMI media supplemented with
  • Each of the cell lines were reverse transfected in 384- well plate format with 25nM of a miRNA from the Dharmacon microRNA mimic or inhibitor libraries (version 16, containing 1280 constructs) using Dharmafect 1 (DF1) transfection reagent according to the manufacturer's instructions for reverse transfection and the conditions described in Table 3. Reverse transfections were performed using liquid-handling robot Calliper Sciclone ALH3000.
  • This screen identified two classes of miRNA:
  • Lethal miRNAs identified in the primary screen are identified in Table 1.
  • miRNAs in rows 1-7, 222, 223, 282-290, 297-312 and 320-329 of Table 1 were found to be lethal in BT-474 cells.
  • miRNAs in rows 8, 291-296 and 313-329 of Table 1 were found to be lethal in SKBR3 cells.
  • miRNAs in rows 9-18, 222-281 and 297-329 of Table 1 were found to be lethal in MDA-MB-231 cells.
  • miRNAs in rows 19-221 and 224-329 of Table 1 were found to be lethal in MDA-MB-468 cells.
  • miRNAs in rows 22 and 23 of Table 1 were found to be lethal in MDA-MB-231 cells and BT-474 cells.
  • miRNAs in rows 224-281 of Table 1 were found to be lethal in MDA-MB-231 cells and MDA-MB-468 cells.
  • miRNAs in rows 282-290 of Table 1 were found to be lethal in BT-474 cells and MDA-MB-468 cells.
  • miRNAs in rows 291-296 of Table 1 were found to be lethal in SKBR3 cells and MDA-MB-468 cells.
  • miRNAs in rows 297-312 of Table 1 were found to be lethal in MDA-MB-468 cells, MDA-MB-231 cells and BT- 474 cells.
  • miRNAs in rows 314-319 of Table 1 were found to be lethal in MDA-MB- 468 cells, MDA-MB-231 cells and SKBR3 cells.
  • the miRNA in row 320 of Table 1 was found to be lethal in MDA-MB-468 cells, BT-474 cells and SKBR3 cells. miRNAs in rows 321-329 of Table 1 were found to be lethal in MDA-MB-468 cells, MDA-MB-231 cells, BT-474 cells and SKBR3 cells.
  • Synthetic lethal miRNAs identified for each cell line in the primary screen are identified in Table 2. Importantly, there were more than 145 miRNAs with synthetic lethal activity in at least one of the breast cancer cell lines, particularly in triple- negative cell lines MDA-MB-231 and MDA-MB-468.
  • Figure 1 is a representative plot illustrating the distribution of miRNAs identified as being lethal and synthetic lethal in MDA-MB-231 cells.
  • the candidates either showed specificity for one drug (either epirubicin or docetaxel) or they synergised with both drugs independently regardless of their mechanism of action. A secondary screen was therefore performed and this confirmed the high reproducibility of this assay and potency of the main microRNA candidates identified.
  • Example 1 the inventors validated a subset of miRNAs identified in Example 1 as being 'synthetic lethal' in further TNBC cell lines.
  • MDA-MB-436, HS578T, and HCC70 were obtained from American Type Culture Collection (ATCC). Each of these cell lines were cultured and treated in accordance with the methods and conditions described in Example 1, albeit using miRNAs described in Table 2 which were identified in Example 1 as being lethal to breast cancer cells when administered in combination with low dose chemotherapy i.e., ' SL-miRs'.
  • a CellTiter-Glo luminescent assay Pro mega was then performed in accordance with Example 1 to determine cell viability. Raw viability was normalised to a nontargeting control (OTP).
  • the miRNAs provided in rows 1-55 of Table 2 were shown to exhibit synthetic lethal activity in at least one of the TNBC cell lines MDA-MB-436, HS578T, and HCC70.
  • the miRNAs that consistently exhibited synthetic lethal activity across the breast cancer cell lines were miR-199a-5p, miR-29b-2-5p, miR-3151, miR-27a-3p, and miR-27b-3p ( Figure 2). These miRNA mimics were each synergising particularly well with epirubicin, but also showed significant activity with docetaxel.
  • Example 3 microRNA (“miR”) expression in clinical samples from breast cancer patients
  • the inventors also analysed changes in miR expression levels in clinical samples obtained from breast cancer patients with TNBC that underwent neoadjuvant chemotherapy, which included alternate cycles of FEC (anthracyclines) and docetaxel (taxane).
  • the clinical samples were obtained from the lead investigator on the ' SETUP' trial, run out of Monash Health in Victoria, Australia.
  • the snap frozen biopsy samples underwent Taqman Q-RT- PCR analysis normalising to RNU19 control RNA for candidate microRNAs described herein.
  • Matched samples from 5 patients that subsequently had a pathological complete response (pCR) and 9 patients that failed to fully repond were analysed.
  • two of the SL-miRs identified in the screens performed in Examples 1 and 2 miR- 199a-5p and miR-29b-2-5p, were found to exhibit increased expression from baseline to the midpoint sample in patients that achieved pathological complete response (pCR) after their chemotherapy treatment (Figure 3). This suggests that the ability of cancers to upregulate these microRNAs correlates with effectiveness of chemotherapy and is consistent with evidence in this study that these microRNAs sensitise cells to chemotherapy.
  • the inventors performed phenotypic assays to verify its effect and investigate the underlying cellular and molecular mechanism of action.
  • MDA-MB-231 cells were cultured in RPMI media supplemented with 10% FCS, HEPES and insulin, and transfected with 25nM of miR-199a-5p mimic or miR-29b-2-5p mimic in a 6-well format using Dharmafect 1 (DF1) transfection reagent according to the manufacturer's instructions. 48 hours post-transfection, cells were treated with epirubicin (IC30) or vehicle control and culturing continued.
  • DF1 Dharmafect 1
  • miR-29b-2-5p was shown to kill MDA-MB-231 cells effectively when applied together with epirubicin. miR-29b-2-5p was also shown to enhance the ability of epirubicin to kill MDA-MB-231 cells compared to epirubicin alone.
  • anthracyclines such as epirubicin
  • the inventors investigated the effect of miR-29b-2-5p and miR-199a-5p mimics on epirubicin-induced cell cycle blocking and DNA damage.
  • MDA-MB-231 cells were cultured in RPMI media supplemented with
  • MDA- MB-231 cells were transfected with miR-199a-5p and miR-29b-2-5p mimics and RNA sequencing was performed.
  • MDA-MB-231 cells were cultured in RPMI media supplemented with 10% FCS, HEPES and insulin, and transfected with 25nM of miR-199a-5p mimic or miR-29b-2-5p mimic in a 6-well format using Dharmafect 1 (DF1) transfection reagent according to the manufacturer's instructions. 72h hours post-transfection, the cells were harvested and RNA sequencing was performed using TruSeq Stranded Total RNA Library Prep kit and HiSeq 2500 sequencing system. Using the RNA sequence data, searches for direct targets among significantly down-regulated genes were performed by applying the following filters:
  • Example 1 The same experiment was performed with several microRNAs that were shown not to have any effect on survival of breast cancer cells in the primary screens performed in Example 1 (i.e., negative miRs), and the direct and indirect targets identified for those negative miRs was used to refine the target list of the SL-miRs i.e., in filter step 4 as described above.
  • the targets identified were: APBB 1, CLIPl, EGF, ETS 1, HAUS5, LIF, MAP3K11, MARK4, MRPS35, OSGIN2, PDCD4, RAD23B, RASSF2, RB I, RBB4, TET2, TGFA, TXNDC12, UNG and XRCC4.
  • the targets identified were: APBB2, APLF, CCNK, HDAC1, MDC1, PTPN11, TGFA, TLK1, TOP2A, TP53, NEK6, ZAK and XRCC4.
  • This screen identified 13 targets that, when depleted via siRNA, have a strong synthetic lethal interaction (defined as > 50% reduction in viability compared to drug alone) with both drugs, four with Epirubicin only, and six with docetaxel only. These data are presented in Table 4 below.
  • the inventors sought to determine whether miRNAs identified in the functional screens are toxic to non-cancer cells.
  • the cell toxicity screens were performed in IMR-90 cells (normal human fibroblast cells, ATCC) for the miRs described in Tables 1 and 2. Briefly, the IMR-90 cells were cultured in MEM media supplemented with 10% FCS, NEAA and sodium pyruvate and miRNA screens were performed with and without the hsa-miRs in accordance with the methods described previously in Examples 1 and 2. Results
  • the toxicity screens showed that many of the miRNAs in Tables 1 and 2 do not significantly affect viability of non-cancerous cells.
  • the toxicity screens showed that hsa-miR-27a-3p and hsa-miR-27b-3p, two miRNAs which consistently exhibited synthetic lethal activity across the breast cancer cell lines, do significantly affect viability of non-cancerous IMR-90 cells.

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Abstract

L'invention concerne des réactifs d'interférence ARN (ARNi) pour le traitement du cancer du sein, des compositions les comprenant, et leur utilisation pour traiter des idividus atteints d'un cancer du sein en tant que monothérapie ou en combinaison avec un agent chimiothérapeutique. En particulier, la présente invention concerne des microARN (miARN) qui affectent la viabilité des cellules du cancer du sein.
PCT/AU2017/050766 2016-07-25 2017-07-25 Méthodes de traitement du cancer du sein et réactifs à cet effet Ceased WO2018018077A1 (fr)

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AU2016902908A AU2016902908A0 (en) 2016-07-25 Methods of treating breast cancer and reagents therefor

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WO2018181877A1 (fr) * 2017-03-30 2018-10-04 株式会社キャンサーステムテック INHIBITEUR DE CROISSANCE DE CELLULES SOUCHES CANCÉREUSES AU MOYEN DE miARN
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